(1) Java
License4J (www.license4j.com) is a Java library for java software licensing. It is designed to be easy to use and integrate in your Java application. Unlike other licensing libraries it has many licensing features defined and performs validation on required features.
License4J comes with a License Manager GUI application to create and store keys and software licenses.
License4J already includes many license features which each business may need.
Implemented features are listed below, only issue date and license id are required features and they are auto created from current system time, all other features are optional.
• Product Features
o Name
o ID
o Version
o Edition
• License Features
o ID
o Issue Date
o Expire Days
o Maintenance Expire Days
o Valid Product Version
o Registered To
• User Features
o Full Name
o E-Mail
o Company
o Telephone
o Fax
o Street
o City
o Zip Code
o Country
• Hardware Feature
2 : License of SVM-light
(2): SVM-Light
---------
Available at http://www-ai.cs.uni-dortmund.de/svm_light
Author: Thorsten Joachims
Joachims@ls8.cs.uni-dortmund.de
Universitaet Dortmund
AI-Unit, Prof. Morik
Baroper Str. 301
44221 Dortmund
Germany
LICENSING TERMS
This program is granted free of charge for research and education
purposes. However you must obtain a license from the author to use it
for commercial purposes.
Scientific results produced using the software provided shall
acknowledge the use of SVM-Light. Please cite as
T. Joachims, Making large-Scale SVM Learning
Practical. Advances in Kernel Methods - Support Vector
Learning, B. Schölkopf and C. Burges and A. Smola (ed.),
MIT-Press, 1999.
http://www-ai.cs.uni-dortmund.de/DOKUMENTE/joachims_99a.pdf
Moreover shall the author of SVM-Light be informed about the
publication.
The software must not be modified and distributed without prior
permission of the author.
By using SVM-Light you agree to the licensing terms.
NO WARRANTY
BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT
WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER
PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND,
EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF
THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO
LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY
OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED
OF THE POSSIBILITY OF SUCH DAMAGES.
(3) Weka
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for software and other kinds of works.
The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions.
Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS
0. Definitions.
“This License” refers to version 3 of the GNU General Public License.
“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.
To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work.
A “covered work” means either the unmodified Program or a work based on the Program.
To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
1. Source Code.
The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.
A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.
The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
The Corresponding Source for a work in source code form is that same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
3. Protecting Users' Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:
a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”.
c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.
A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.
“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
7. Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.
All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
11. Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see .
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read .
(4) R Package
R as a package is licensed under GPL-2 | GPL-3. File doc/COPYING is the same as GPL-2.
Some files are licensed under 'GPL (version 2 or later)', which includes GPL-3. See the comments in the files to see if this applies.
Some header files are distributed under LGPL-2.1: see file COPYRIGHTS (on the SVN server).
(5) HHsuite
Copyright for “hhsuite” source package in Quantal
Ubuntu
Quantal (12.10)
“hhsuite” source package
Copyright
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: hhsuite
Upstream-Contact: Andreas Hauser
Johannes Soeding
Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz
Files: src/fmemopen.c src/fmemopen.h lib/ffindex/src/ext/fmemopen.c lib/ffindex/src/ext/fmemopen.h
Copyright: 2009 Open Information Security Foundation
License: GPL-2.0+
Files: src/cs/getopt_pp.h src/cs/getopt_pp.cc
Copyright: 2007, 2008 Daniel Gutson, FuDePAN
License: GPL-3.0+
Files: src/pngwriter.cc src/pngwriter.h
Copyright: 2002, 2003 Paul Blackburn
License: GPL-2.0+
Files: lib/ffindex/*
Copyright: Andy Hauser
License: CC-BY-SA-3.0
Files: debian/*
Copyright: 2012 Laszlo Kajan
License: GPL-3.0+
Files: *
Copyright: 2006, 2012 Johannes Soeding
2012 Michael Remmert
2012 Andreas Hauser
2006, 2009, 2012 Andreas Biegert
License: GPL-3.0+
License: CC-BY-SA-3.0
Create Commons license "Attribution-ShareAlike 3.0"
.
See: http://creativecommons.org/licenses/by-sa/3.0/
.
Basically you are free:
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* to Share — to copy, distribute and transmit the work
* to Remix — to adapt the work
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Under the following conditions:
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* Attribution
You must attribute the work in the manner specified by the author or
licensor (but not in any way that suggests that they endorse you or your
use of the work).
* Share Alike
If you alter, transform, or build upon this work, you may distribute the
resulting work only under the same or similar license to this one.
License: GPL-2.0+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
License: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
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This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
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On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
(6) Modeller
Accelrys licensing
MODELLER is available free of charge to academic non-profit institutions (you will, however, need to register for a license).
For commercial entities or government research labs (such as the NIH and national labs in the USA), MODELLER is available from Accelrys. For further details, please contact Accelrys Inc., 10188 Telesis Ct., San Diego, CA 92121, USA, email support@accelrys.com.
Accelrys also makes commercially available several graphical interfaces to MODELLER. Teaching licenses are available to those institutions that acquire and maintain a research license.
(7) SNNS License
This License Agreement applies to the SNNS program and all accompanying programs and files that are distributed with a notice placed by the copyright holder saying it may be distributed under the terms of the SNNS License. ``SNNS'', below, refers to any such program or work, and a ``work based on SNNS'' means either SNNS or any work containing SNNS or a portion of it, either verbatim or with modifications. Each licensee is addressed as ``you''.
You may copy and distribute verbatim copies of SNNS's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of SNNS a copy of this license along with SNNS.
You may modify your copy or copies of SNNS or any portion of it only for your own use. You may not distribute modified copies of SNNS. You may, however, distribute your modifications as separate files (e.g. patch files) along with the unmodified SNNS software. We also encourage users to send changes and improvements which would benefit many other users to us so that all users may receive these improvements in a later version. The restriction not to distribute modified copies is also useful to prevent bug reports from someone else's modifications.
If you distribute copies of SNNS you may not charge anything except the cost for the media and a fair estimate of the costs of computer time or network time directly attributable to the copying.
You may not copy, modify, sub-license, distribute or transfer SNNS except as expressly provided under this License. Any attempt otherwise to copy, modify, sub-license, distribute or transfer SNNS is void, and will automatically terminate your rights to use SNNS under this License. However, parties who have received copies, or rights to use copies, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.
By copying, distributing or modifying SNNS (or any work based on SNNS) you indicate your acceptance of this license to do so, and all its terms and conditions.
Each time you redistribute SNNS (or any work based on SNNS), the recipient automatically receives a license from the original licensor to copy, distribute or modify SNNS subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein.
Incorporation of SNNS or parts of it in commercial programs requires a special agreement between the copyright holder and the Licensee in writing and usually involves the payment of license fees. If you want to incorporate SNNS or parts of it in commercial programs write to the author about further details.
Because SNNS is licensed free of charge, there is no warranty for SNNS, to the extent permitted by applicable law. The copyright holders and/or other parties provide SNNS ``as is'' without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of SNNS is with you. Should the program prove defective, you assume the cost of all necessary servicing, repair or correction.
In no event will any copyright holder, or any other party who may redistribute SNNS as permitted above, be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use SNNS (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of SNNS to operate with any other programs), even if such holder or other party has been advised of the possibility of such damages.
(8) PERL
GNU GENERAL PUBLIC LICENSE
Version 1, February 1989
Copyright (C) 1989 Free Software Foundation, Inc.
51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The license agreements of most software companies try to keep users
at the mercy of those companies. By contrast, our General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. The
General Public License applies to the Free Software Foundation's
software and to any other program whose authors commit to using it.
You can use it for your programs, too.
When we speak of free software, we are referring to freedom, not
price. Specifically, the General Public License is designed to make
sure that you have the freedom to give away or sell copies of free
software, that you receive source code or can get it if you want it,
that you can change the software or use pieces of it in new free
programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of a such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must tell them their rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
software. If the software is modified by someone else and passed on, we
want its recipients to know that what they have is not the original, so
that any problems introduced by others will not reflect on the original
authors' reputations.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any program or other work which
contains a notice placed by the copyright holder saying it may be
distributed under the terms of this General Public License. The
"Program", below, refers to any such program or work, and a "work based
on the Program" means either the Program or any work containing the
Program or a portion of it, either verbatim or with modifications. Each
licensee is addressed as "you".
1. You may copy and distribute verbatim copies of the Program's source
code as you receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice and
disclaimer of warranty; keep intact all the notices that refer to this
General Public License and to the absence of any warranty; and give any
other recipients of the Program a copy of this General Public License
along with the Program. You may charge a fee for the physical act of
transferring a copy.
2. You may modify your copy or copies of the Program or any portion of
it, and copy and distribute such modifications under the terms of Paragraph
1 above, provided that you also do the following:
a) cause the modified files to carry prominent notices stating that
you changed the files and the date of any change; and
b) cause the whole of any work that you distribute or publish, that
in whole or in part contains the Program or any part thereof, either
with or without modifications, to be licensed at no charge to all
third parties under the terms of this General Public License (except
that you may choose to grant warranty protection to some or all
third parties, at your option).
c) If the modified program normally reads commands interactively when
run, you must cause it, when started running for such interactive use
in the simplest and most usual way, to print or display an
announcement including an appropriate copyright notice and a notice
that there is no warranty (or else, saying that you provide a
warranty) and that users may redistribute the program under these
conditions, and telling the user how to view a copy of this General
Public License.
d) You may charge a fee for the physical act of transferring a
copy, and you may at your option offer warranty protection in
exchange for a fee.
Mere aggregation of another independent work with the Program (or its
derivative) on a volume of a storage or distribution medium does not bring
the other work under the scope of these terms.
3. You may copy and distribute the Program (or a portion or derivative of
it, under Paragraph 2) in object code or executable form under the terms of
Paragraphs 1 and 2 above provided that you also do one of the following:
a) accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of
Paragraphs 1 and 2 above; or,
b) accompany it with a written offer, valid for at least three
years, to give any third party free (except for a nominal charge
for the cost of distribution) a complete machine-readable copy of the
corresponding source code, to be distributed under the terms of
Paragraphs 1 and 2 above; or,
c) accompany it with the information you received as to where the
corresponding source code may be obtained. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form alone.)
Source code for a work means the preferred form of the work for making
modifications to it. For an executable file, complete source code means
all the source code for all modules it contains; but, as a special
exception, it need not include source code for modules which are standard
libraries that accompany the operating system on which the executable
file runs, or for standard header files or definitions files that
accompany that operating system.
4. You may not copy, modify, sublicense, distribute or transfer the
Program except as expressly provided under this General Public License.
Any attempt otherwise to copy, modify, sublicense, distribute or transfer
the Program is void, and will automatically terminate your rights to use
the Program under this License. However, parties who have received
copies, or rights to use copies, from you under this General Public
License will not have their licenses terminated so long as such parties
remain in full compliance.
5. By copying, distributing or modifying the Program (or any work based
on the Program) you indicate your acceptance of this license to do so,
and all its terms and conditions.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the original
licensor to copy, distribute or modify the Program subject to these
terms and conditions. You may not impose any further restrictions on the
recipients' exercise of the rights granted herein.
7. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of the license which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
the license, you may choose any version ever published by the Free Software
Foundation.
8. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
9. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
Appendix: How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to humanity, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.
To do so, attach the following notices to the program. It is safest to
attach them to the start of each source file to most effectively convey
the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
Copyright (C) 19yy
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 1, or (at your option)
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA
02110-1301 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) 19xx name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type 'show c' for details.
The hypothetical commands 'show w' and 'show c' should show the
appropriate parts of the General Public License. Of course, the
commands you use may be called something other than 'show w' and 'show
c'; they could even be mouse-clicks or menu items--whatever suits your
program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
program 'Gnomovision' (a program to direct compilers to make passes
at assemblers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
That's all there is to it!
(10) Galaxy Tool
Galaxytool License
Copyright (c) 2005-2013 by Christian Lehmann
www.galaxytool.eu
webmaster @ mathe-informatik.de
This licence agreement does apply to Galaxytool itself as well as the Galaxytool toolbar (both below: Galaxytool)
Galaxytool is not open source. Code changes are prohibited.
It is strictly forbidden to distribute Galaxytool or modified versions. Galaxytool shall only be obtained from www.galaxytool.eu.
At most 10 Galaxytools may be hosted per individual. Hosting of more tools requires explicit permission.
It is strictly prohibited to automate Galaxytool in any way.
Galaxytool is for private use only. Commercial use, no matter in which way (e.g. selling of expansions or modifications, advertised hosting, selling of data acquired by Galaxytool) is strictly prohibited.
Claims related to No.4 or 5 of this licence agreement are transferred to Gameforge AG, Germany and will be enforced by law.
(11) Open-babel with python
GNU Free Documentation License
Version 1.3, 3 November 2008
Copyright © 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
0. PREAMBLE
The purpose of this License is to make a manual, textbook, or other functional and useful document "free" in the sense of freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications made by others.
This License is a kind of "copyleft", which means that derivative works of the document must themselves be free in the same sense. It complements the GNU General Public License, which is a copyleft license designed for free software.
We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference.
1. APPLICABILITY AND DEFINITIONS
This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration, to use that work under the conditions stated herein. The "Document", below, refers to any such manual or work. Any member of the public is a licensee, and is addressed as "you". You accept the license if you copy, modify or distribute the work in a way requiring permission under copyright law.
A "Modified Version" of the Document means any work containing the Document or a portion of it, either copied verbatim, or with modifications and/or translated into another language.
A "Secondary Section" is a named appendix or a front-matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document's overall subject (or to related matters) and contains nothing that could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of legal, commercial, philosophical, ethical or political position regarding them.
The "Invariant Sections" are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any Invariant Sections then there are none.
The "Cover Texts" are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that says that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may be at most 25 words.
A "Transparent" copy of the Document means a machine-readable copy, represented in a format whose specification is available to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not "Transparent" is called "Opaque".
Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input format, SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally available, and the machine-generated HTML, PostScript or PDF produced by some word processors for output purposes only.
The "Title Page" means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material this License requires to appear in the title page. For works in formats which do not have any title page as such, "Title Page" means the text near the most prominent appearance of the work's title, preceding the beginning of the body of the text.
The "publisher" means any person or entity that distributes copies of the Document to the public.
A section "Entitled XYZ" means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as "Acknowledgements", "Dedications", "Endorsements", or "History".) To "Preserve the Title" of such a section when you modify the Document means that it remains a section "Entitled XYZ" according to this definition.
The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.
2. VERBATIM COPYING
You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough number of copies you must also follow the conditions in section 3.
You may also lend copies, under the same conditions stated above, and you may publicly display copies.
3. COPYING IN QUANTITY
If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the Document's license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects.
If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably) on the actual cover, and continue the rest onto adjacent pages.
If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-readable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from which the general network-using public has access to download using public-standard network protocols a complete Transparent copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public.
It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document.
4. MODIFICATIONS
You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the Modified Version:
A. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous versions (which should, if there were any, be listed in the History section of the Document). You may use the same title as a previous version if the original publisher of that version gives permission.
B. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the Modified Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has fewer than five), unless they release you from this requirement.
C. State on the Title page the name of the publisher of the Modified Version, as the publisher.
D. Preserve all the copyright notices of the Document.
E. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices.
F. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version under the terms of this License, in the form shown in the Addendum below.
G. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document's license notice.
H. Include an unaltered copy of this License.
I. Preserve the section Entitled "History", Preserve its Title, and add to it an item stating at least the title, year, new authors, and publisher of the Modified Version as given on the Title Page. If there is no section Entitled "History" in the Document, create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the Modified Version as stated in the previous sentence.
J. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and likewise the network locations given in the Document for previous versions it was based on. These may be placed in the "History" section. You may omit a network location for a work that was published at least four years before the Document itself, or if the original publisher of the version it refers to gives permission.
K. For any section Entitled "Acknowledgements" or "Dedications", Preserve the Title of the section, and preserve in the section all the substance and tone of each of the contributor acknowledgements and/or dedications given therein.
L. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the equivalent are not considered part of the section titles.
M. Delete any section Entitled "Endorsements". Such a section may not be included in the Modified Version.
N. Do not retitle any existing section to be Entitled "Endorsements" or to conflict in title with any Invariant Section.
O. Preserve any Warranty Disclaimers.
If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to the list of Invariant Sections in the Modified Version's license notice. These titles must be distinct from any other section titles.
You may add a section Entitled "Endorsements", provided it contains nothing but endorsements of your Modified Version by various parties—for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard.
You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one.
The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version.
5. COMBINING DOCUMENTS
You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.
The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.
In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements".
6. COLLECTIONS OF DOCUMENTS
You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.
You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.
7. AGGREGATION WITH INDEPENDENT WORKS
A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.
If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document's Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate.
8. TRANSLATION
Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.
If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.
9. TERMINATION
You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense, or distribute it is void, and will automatically terminate your rights under this License.
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, receipt of a copy of some or all of the same material does not give you any rights to use it.
10. FUTURE REVISIONS OF THIS LICENSE
The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See http://www.gnu.org/copyleft/.
Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version of this License "or any later version" applies to it, you have the option of following the terms and conditions either of that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation. If the Document specifies that a proxy can decide which future versions of this License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Document.
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"Massive Multiauthor Collaboration Site" (or "MMC Site") means any World Wide Web server that publishes copyrightable works and also provides prominent facilities for anybody to edit those works. A public wiki that anybody can edit is an example of such a server. A "Massive Multiauthor Collaboration" (or "MMC") contained in the site means any set of copyrightable works thus published on the MMC site.
"CC-BY-SA" means the Creative Commons Attribution-Share Alike 3.0 license published by Creative Commons Corporation, a not-for-profit corporation with a principal place of business in San Francisco, California, as well as future copyleft versions of that license published by that same organization.
"Incorporate" means to publish or republish a Document, in whole or in part, as part of another Document.
An MMC is "eligible for relicensing" if it is licensed under this License, and if all works that were first published under this License somewhere other than this MMC, and subsequently incorporated in whole or in part into the MMC, (1) had no cover texts or invariant sections, and (2) were thus incorporated prior to November 1, 2008.
The operator of an MMC Site may republish an MMC contained in the site under CC-BY-SA on the same site at any time before August 1, 2009, provided the MMC is eligible for relicensing.
ADDENDUM: How to use this License for your documents
To use this License in a document you have written, include a copy of the License in the document and put the following copyright and license notices just after the title page:
Copyright (C) YEAR YOUR NAME.
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the section entitled "GNU
Free Documentation License".
If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the "with … Texts." line with this:
with the Invariant Sections being LIST THEIR TITLES, with the
Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit the situation.
If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your choice of free software license, such as the GNU General Public License, to permit their use in free software.
(12) Babel
Copyright © 2007-2012 Edgewall Software[[BR]]
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution.
3. The name of the author may not be used to endorse or promote
products derived from this software without specific prior
written permission.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR “AS IS” AND ANY EXPRESS
OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
(13) Ant
What licensing requirements apply to working with ANT?
Hardware licensing
Use of devices such as Nordic Semiconductor’s nRF24AP2 and TI’s CC257x, and the related modules in a design does not require a license.
Enabling ANT on TI multi-protocol devices and related modules does require a license. Please contact Dynastream for the details on enabling ANT on these platforms.
Network Keys
If you are building a non-ANT+ product (i.e. an ANT product that does not implement an ANT+ Device Profile) you may not use the ANT+ network key or the ANT+ frequency (2457MHz). You may use any other frequency and either the public network key or a private network key.
ANT+
If you are building a product that is intended to interoperate with other ANT+ devices or applications, you’ll find our ANT+ Device Profiles, and an array of design tools, on the downloads page. Items marked with the ANT+ logo are only accessible to ANT+ Adopters. You can access them by signing up (for free!) to become an ANT+ Adopter, here: ANT+ Adopter sign-up. This will also give you access to a lot of good ANT+ forum advice, and the ANT+ network key.
To participate in the development of new ANT+ device profiles, gain direct technical support, and participate in B2B opportunities such as the ANT+ Symposium; see ANT+ Alliance Membership.
Software
Openly available software posted on our downloads page comes with the Apache 2.0 license or the FIT protocol license. We’d like you to use the code, recognizing the value of maintaining interoperability.
Software marked with an ANT+ icon; (and only accessible to ANT+ Adopters) is covered by the ANT+ shared source license. Please check this for details and restrictions, however in general you are free to use the reference code within your commercial ANT+ products.
(14) CDK
Apache License
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APPENDIX: How to apply the Apache License to your work.
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(15) MEME/MAST
MEME SUITE 4.X
SITE LICENSE AGREEMENT
THIS AGREEMENT ("Agreement") is made by and between having a principal place of business at
,
("LICENSEE") and The Regents of the University of California, a California corporation having its statewide administrative offices at 1111 Franklin Street, 12th Floor, Oakland, California 94607-5200 ("UNIVERSITY"), represented by its San Diego campus having an address at University of California, San Diego, Technology Transfer Office, Mailcode 0910, 9500 Gilman Drive, La Jolla, California 92093-0910 ("UCSD").
This Agreement is effective on the date of the last signature herein executing this Agreement ("Effective Date").
RECITALS
WHEREAS, certain software, entitled "MEME Suite 4.0- "Motif-based sequence analysis tools" and specifically docketed as SD2010-808 was developed in the course of research at UNIVERSITY, The University of Washington and The University of Queensland by Dr. Timothy L. Bailey and associates ("Authors") and is covered by University's Copyrights (as defined below);
WHEREAS, UNIVERSITY, The University of Washington and IMBcom PTY Limited (representing the interest of The University of Queensland) have entered into an agreement whereby UCSD will manage the commercial licensing of University Copyrights on behalf of all Authors and their respective employing institutions;
WHEREAS, this software was developed under sponsoship of the Department of Health and Human Services' ("HHS") and the National Center for Research Resources grant NIH/NCRR R01 RR021692 and as a consequence this agreement and licenses granted are subject to the overriding obligations to HHS under 45 C.F.R. § 74.36, which obligations include a royalty-free, nonexclusive and irrevocable right of HHS to reproduce, publish, or otherwise use it for Federal purposes, and to authorize others to do so ("Sponsor Rights");
WHEREAS, LICENSEE desires to obtain a license to copy, install, and use this software on multiple computers located at the Site(s) specified in Appendix A hereof; and
WHEREAS, UNIVERSITY is willing to grant LICENSEE certain non-exclusive rights to copy, install, and use this software on multiple computers located at the Site(s) specified in
Appendix A.
NOW THEREFORE, the parties hereby agree as follows: ARTICLE 1. DEFINITIONS.
The terms, as defined herein, shall have the same meanings in both their singular and plural forms.
1.1 "Documentation" means information relating to the Licensed Software and found at the internet website having the address, http://meme.nbcr.net/meme/documentation.html.
1.2 "Field" means analysis of macromolecular sequences.
1.3 "Licensed Software" means the computer program entitled " MEME Suite 4.0- "Motif- based sequence analysis tools" and specifically docketed as SD2010-808, and found at
the internet website having the address, http://meme.nbcr.net/meme/meme-downloads.html.
1.4 "Site(s)" means the physical address(es) where Licensed Software will be used by LICENSEE as specified in Appendix A hereof.
1.5 "Term" means the period of time beginning on the Effective Date and ending on the date five (5) years from the Effective Date.
1.6 "University's Copyrights" means all of UNIVERSITY's, The University of Washington’s and IMBcom PTY Limited’s interest in the copyrights, domestic and foreign, subsisting in the source code and object code of Licensed Software, and the Documentation.
ARTICLE 2. GRANT.
2.1 License to Use Software. Subject to the limitations set forth in this Agreement and subject to Sponsor's Rights, UNIVERSITY hereby grants LICENSEE a non-exclusive, non-transferable, license under University' s Copyrights to install and use the Licensed Software in the Field, on all computer systems now or in the future owned or leased by LICENSEE and located at the Site(s) and for the Term, and to use the Documentation in the Field, for the Term, at the Site(s).
2.2 Right to Copy Software. LICENSEE may copy the Licensed Software, in whole or in part, to the extent necessary toexercise the foregoing license, for internal use in testing, training, evaluation and disaster recovery purposes, and for backup and archival
2.3
purposes. LICENSEE shall reproduce the following copyright notice on all copies of the Licensed Software, and all copies shall be subject to all terms, conditions and obligations of this Agreement.
© 2009 The Regents of the University of California, The University of Washington, IMBcom PTY Limited. All Rights Reserved.
Restrictions on Use. The foregoing rights to copy, install, and use the Licensed Software shall be subject to the following restrictions:
(a) LICENSEE shall not copy or allow copies of the Licensed Software to be made, except as specifically allowed under this Agreement;
(b) LICENSEE shall not install the Licensed Software in a single CPU or in a network, multiple CPU or multiple-user arrangement, except within the confines of the Site(s);
(c) LICENSEE shall not use the Licensed Software in a si ngle CPU, in a network, multiple CPU or multiple-user arrangement or through the Internet, except within the confines of the Site(s);
(d) LICENSEE shall not allow third parties (except for independent contractors of LICENSEE) to install the Licensed Software in a single CPU or in a network, multiple CPU or multiple-user arrangement, regardless of whether such installation occurs inside or outside of the confines of the Site(s);
(e) LICENSEE shall not allow third parties (except for independent contractors of LICENSEE) to use the Licensed Software in a single CPU, in a network, multiple CPU or multiple-user arrangement or through the Internet, regardless of whether such use occurs inside or outside of the confines of the Site(s);
2.4
(g) LICENSEE shall not use the Licensed Software through the Internet except between one or more Site(s); and
(h) LICENSEE may modify or alter the Licensed Software, but only to the extent necessary to make the Licensed Software operate on LICENSEE' s computers at the Site(s), and the restrictions of Paragraphs 2.3(a) through 2.3(g) hereof shall apply to the Licensed Software as modified or altered by LICENSEE.
Right to Copy Documentation. LICENSEE may copy the Docu mentation to the extent
(f) LICENSEE shall to any third party;
not res ell, lease, sublicense or distribute th e Licensed Software
necessary to exercise the foregoing license. Licensee shall reproduce the following copyright notice on all copies of the Documentation, and all copies shall be subject to all terms, conditions and obligations of this Agreement.
© 2009 The Regents of the University of California, The University of Washington, IMBcom PTY Limited. All Rights Reserved.
2.5 Right to Grant Sublicenses. The license and right granted in Paragraphs 2.1 and 2.2 includes the right of LICENSEE to grant sublicenses to a third party, who is a service provider to LICENSEE performing certain information technology operations and management services and related ancillary services for LICENSEE pursuant to an arrangement or agreement commonly known in the industry as an outsourcing agreement; provided, however, that such sublicenses shall be in writing and limited to the installation, use and copying of the Licensed Software by such service provider as is necessary for continued operation and management of LICENSEE'scomputers running Licensed Software at the Site(s) and during the Term.
2.6 Right to Change or Add Site(s). LICENSEE may change the location of any Site or add additional Site(s) during the Term by written notice to UCSD made pursuant to Paragraph 10.1 hereof and submission of the necessary additional Si te License Fee per Paragraph 6.1 herein. Upon the effective of date such notice:
(a) the Site(s) as used in this Agreement shall thereafter be defined as the location provided in such notice and, if a change of Site only, the former location shall cease to defined as a Site;
(b) LICENSEE shall cease using the Licensed Software and Documentation at the former location of the Site, if a change of Site only; and
(c) LICENSEE shall remove all copies of the Licensed Software and Documentation from all computer systems at the former location of the Site, if a change of Site only.
ARTICLE 3. OWNERSHIP OF LICENSED SOFTWARE.
3.1 Ownership. LICENSEE acknowledges that the Licensed Software and the Documentation, and all copies thereof made by LICENSEE under this Agreement, are the exclusive and joint property of UNIVERSITY, The University of Washington and IMBcom PTY Limited and title to the Software and Documentation provided under this Agreement and all copies thereof made by LI CENSEE shall at all times remain with UNIVERSITY, The University of Washington and IMBcom PTY Limited or their respective assignee. LICENSEE further acknowledges that LICENSEE has no rights in the Licensed Software except those expressly granted by this Agreement.
3.2 Notices. LICENSEE shall not remove, alter, cover or distort any copyright notice, trademark or other proprietary rights notice placed by UNIVERSITY, The University of
Washington or IMBcom PTY Limited in or on the Licensed Software or Documentation.
ARTICLE 4. DELIVERY OF MASTER COPY.
4.1 Licensed Software and Documentation. LICENSEE may download the Licensed Software and Documentation from UNIVERSITY's internet website having the address, http://meme.nbcr.net/meme/meme-downloads.html.
4.2 Expenses. LICENSEE shall bear the additional expenses of copying and distributing the Licensed Software and its accompanying Documentation for its use within the Site.
ARTICLE 5. INSTALLATION AND SUPPORT.
5.1 Installation. LICENSEE shall assume all responsibility and expense arising from or relating to the installation of the Licensed Software and Documentation at the Site(s). Neither UNIVERSITY, The University of Washington or IMBcom PTY Limited is obligated under this Agreement to provide support to LICENSEE with respect such installation.
5.2 Support. LICENSEE shall assume all responsibility and expense for support arising from or relating to LICENSEE's use of the Licensed Software and Documentation. UNIVERSITY is not obligated under this Agreement to provide support to LICENSEE with respect to such use.
ARTICLE 6. CONSIDERATION.
6.1 Site License Fee. LICENSEE shall pay to UNIVERSIT Y an annual Site License Fee of two-thousand five-hundred dollars (US$2,500.00) for each of the Site(s) listed in Appendix A, or hereafter added to Appendix A as provided for under Paragraph 2.6, according to the Site License Purchase Order, which is Appendix B of this Agreement. Payment of the Site License Fee shall be due within thirty (30) days of the Effective Date and each anniversary thereafter during the Term. License Fees are net of anytaxes imposed by foreign governments. Such taxesshould be added to the amounts given in Appendix B, if applicable.
6.2 Payments. All fees payable to UNIVERSITY under this Agreement shall be paid in United States dollars by check made payable to "The Regents of the University of California", referencing UNIVERSITY's taxpayer identification number, 95-6006144. These payments shall be sent to:
if by US Mail,
University of California, San Diego Technology Transfer Office, Mailcode 0910 9500 Gilman Drive
La Jolla, CA 92093-0910
Attention: Assistant Vice Chancellor
if by courier,
University of California, San Diego Technology Transfer Office
10300 N. Torrey Pines Rd.
1st Floor
La Jolla, CA 92037
Attention: Assistant Vice Chancellor
Fax: 858-534-7345 Phone: 858-534-5815
if by wire transfer (for non-U.S. companies only), there is an additional fee of twenty- five US dollars ($25.00). Electronic Transfer of Fund Information is as follows:
UCSD receiving bank name: UCSD bank account no.: UCSD bank routing (ABA) no.: UCSD bank account name:
UCSD bank ACH format code: CHIPS Address:
UCSD bank address:
UCSD addendum information:
SWIFT Address:
Bank of America 1233018188
0260-0959-3
Regents of the University of California, UCSD Depository CTX
0959
Bank of America
PO Box 37025
San Francisco, CA 94137 U.S.A.
Reference UCSD-TTO Case
No.: SD2010-808
Department contact: Financial Manager BOFAUS3N
A copy of the transaction receipt should be sent to Financial Manager via (a) fax at (858) 534-7345, or (b) e-mail at TTOWire@ucsd.edu. LICENSEE is responsible for all bank charges of wire transfer funds. The bank charges should not be deducted from total amount due to the Regents of the University of California
ARTICLE 7. LIMITED WARRANTY AND INDEMNIFICATION.
7.1 Limited Warranty.
(a) UNIVERSITY warrants that it has the lawful right to grant this license.
(b) The license granted herein, and the Licensed Software and Documentation provided herein, are provided "AS IS" and WITTHOUT WARRANTY OF MERCHANTABILITY or W ARRANTY OF FITNESS FOR A PARTICULAR PURPOSE or any other warranty, express or implied. UNIVERSITY makes no representation or warranty that the Licensed Software or Documentation will not infringe any other patent, copyright or other proprietary rights.
(c) In no event shall UNIVERSITY, T he University of Washington or IMBcom PTY Limited be liable to LICENSEE for any incidental, special or consequential damages to resulting from LICENSEE's exercise of the license granted herein or the use of the Licensed Software or Documentation.
(d) Nothing in this Agreement shall be construed as:
(1) a warranty or representation by UNIVERSITY, The University of Washington or IMBcom PTY Limited as to the validity or scope of any University's Copyrights;
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under any patent rights or copyrights of UNIVERSITY, The University of Washington or IMBcom PTY Limited, other than University's Copyrights as defined in this Agreement, regardless of whether those copyrights are dominant or subordinate to University's Copyrights; or
(5) an obligation to provide fixes or updates to Licensed Software.
7.2 Indemnity.
(a) LICENSEE shall indemnify, hold harmless and defend UNIVERSITY, The University of Washington and IMBcom PTY Limited, its officers, employees, and agents; thesponsorsoftheresearchthatledtotheLicensedSoftwareand
Documentation; and the Authors and their employers against any and all claims, suits, actions, and proceedings ("Claim s") arising out of the exercise of any right granted under this Agreement, including without limitation, the generality of the forgoing against any damages, losses, liabilities, costs or expenses including reasonable attorney's fees whatsoever with respect to death or injury to person or to damage to property arising fromor out of the possession, use or operation of Licensed Software and Documentation by LICENSEE.
(b) UNIVERSITY shall promptly notify LICENSEE in writing of any claim or suit brought against UNIVERSITY, The University of Washington or IMBcom PTY Limited in respect of which UNIVERSITY intends to invoke the provisions of this Article. LICENSEE shall keep UNIVERSITY informed on a current basis of its defense of any claims under Paragraph 7.2(a) hereof.
ARTICLE 8. TERM AND TERMINATION.
8.1 Term. The license granted under this Agreement shall continue for the Term, unless
sooner terminated by UNIVERSITY or LICENSEE in accordance with this Agreement.
8.2 Termination.
(a) Termination by University. If LICENSEE fails to perform or violates any term of this Agreement, then UNIVERSITY may give written notice of default ("Notice of Default") to LICENSEE. If LICENSEE fails to cure the default withinsixty(60) days of the effective date of Notice of Default, UNIVERSITY may terminate this Agreement and the license granted herein by a second written notice ("Notice of Termination") to LICENS EE. If a Notice of Termination is sent to LICENSEE, this Agreement and the license granted herein shall automatically terminate on the effective date of that notice. Termination shall not relieve LICENSEE of its obligation to pay any monies owing at the time of termination and shall not impair any accrued right of UNIVERSITY. These notices are subject to Paragraph 10.1 (Notices) hereof.
(b) Termination by Licensee. LICENSEE shall have the right at any time to terminate this Agreement and the license granted herein by giving notice in writing to UNIVER SITY. Notice of termination shall be subject to Paragraph 10.1 (Notices) hereof, and such termination of this Agreement and the license granted herein shall be effective thirty (30) days from the effective date of notice. Any termination under this paragraph shall not relieve LICENSEE of any obligation owed to UNIVERSITY or liability accrued in favor of UNIVERSITY under this Agreement prior to termination or rescind any payment made to UNIVERSITY or anything done by LICENSEE under this Agreement prior to the time termination becomes effective.
8.3 Events upon Termination. Upon termination of this Agreement and the license granted hereunder, LICENSEE shall:
(a) immediately cease using the Licensed Software and Documentation;
(b) immediately remove all copies of the Licensed Software and Documentation from all computer systems at the Site; and
(c) within thirty (30) days of the date of such termination, return to UNIVERSITY the Licensed Software and Documentation and copies thereof then in LICENSEE's possession.
8.4 Survival. Any termination of this Agreement shall not affect the rights and obligations set forth in the following paragraphs or Articles:
(a) Article 7 (Limited Warranty and Indemnification);
(b) Paragraph 8.3 (Events upon Termination); and
(c) Article 9 (USE OF NAMES AND TRADEMARKS).
ARTICLE 9. USE OF NAMES AND TRADEMARKS.
9.1 Nothing contained in this Agreement confers any right to use in advertising, publicity, or other promotional activities any name, trade name, trademark, or other designation of either party hereto (including contraction, abbreviation or simulation of any of the foregoing). Unless required by law, the use by LICENSEE of the name, "The Regents of The University of California" or the name of any campus of the University of California, the use by LICENSEE of the name “The University of Washington” or the name of any campus of The University of Washington, or the name “IMBcom PTY Limited” or the use by UNIVERSITY of the name of
is prohibited, without the express written consent of UNIVERSITY or LICENSEE, as the case may be.
9.2 UNIVERSITY may acknowledge the existence of this Agreement and the extent of the grant in Article 2 (GRANT) to third parties, but UNIVERSITY shall not disclose the financial terms of this Agreement to third parties, except where UNIVERSITY is required by law to do so, such as under the California Public Records Act, or the Public Records Act RCW 52.56 of State of Washington .
ARTICLE 10. MISCELLANEOUS PROVISIONS.
10.1 Notices. Except as otherwise provided in this Agreement, any notice or payment
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If to LICENSEE: (Enter name and address)
Attention: Phone: Facsimile:
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University of California, San Diego Technology Transfer Office, Mailcode 0910 9500 Gilman Drive
La Jolla, CA 92093-0910
Attention: Assistant Vice Chancellor
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University of California, San Diego Technology Transfer Office
10300 N. Torrey Pines Rd.
1st Floor
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Attention: Assistant Vice Chancellor
Fax:
Phone: 858-534-5815
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or to such other address or individual as either party may specify from time to time by written notice given by such party.
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10.7 Headings. The headings of the several sections are inserted for convenience of reference only and are not intended to be a part of or to affect the meaning or interpretation of this Agreement.
10.8 Entire Agreement. This Agreement embodies the entire understanding of the parties and supersedes all previous communication, representations or understandings, either oral or written, between the parties relating to the subject matter hereof.
10.9 Amendments. No amendment or modification of this Agreement shall be valid or binding on the parties unless made in writing and signed on behalf of each party.
10.10 Severability. In the event that any of the provisions contained in this Agreement is held to be invalid, illegal, or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, and this Agreement shall be construed as if the invalid, illegal, or unenforceable provisions had never been contained in it.
10.11 Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument.
THE REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK
IN WITNESS WHEREOF, the parties have caused this Agreement to be executed in duplicate originals by their duly authorized representatives.
LICENSEE:
By______________________________ (Signature)
Name: Title:
Date______________________________
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA:
By_________________________ (Signature)
Jane C. Moores, PhD
Assistant Vice Chancellor, Technology Transfer Office
Date_________________________
THE REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK
Appendix A
Site(s) of Installation of Licensed Software: Site #1
Site #2
Site #3
Site #4
[continue on additional sheets as needed.]
Appendix B
Site License Purchase Order
Agreement #:__________________________ (UCSD use only) Licensee Name:
Licensee Address:
Number of Site(s) requested in Appendix A: _______
Multiplied by annual site license fee: Total annual license fee:
x $2,500.00 =________
(16) MPIblast
Copyright
Copyright 2008 by Virginia Polytechnic Institute and State University. All rights reserved. Virginia Polytechnic Institute and State University (Virginia Tech) owns the mpiBLAST software and its associated documentation (“Software”). You should carefully read the following terms and conditions before using this software. Your use of this Software indicates your acceptance of this license agreement and all terms and conditions.
The parallel input/output (PIO) portion of this work was based in part on published research that was supported by the North Carolina State University and Oak Ridge National Laboratory. The actual implementation was completed at Virginia Tech in the summer of 2007.
Additionally, portions of this work are derivative works of the NCBI C Toolkit. Although, the NCBI C Toolkit is released freely without restriction under the terms of their license, the following files listed below, have been modified by Virginia Tech, and as such are redistributed under the terms of this license.
ncbi/api/txalign.c
ncbi/corelib/ncbifile.c
ncbi/object/objalign.c
ncbi/tools/blast.c
ncbi/tools/blastdef.h
ncbi/tools/blastool.c
ncbi/tools/blastutl.c
ncbi/tools/blfmtutl.c
ncbi/tools/ncbisam.c
ncbi/tools/readdb.c
ncbi/tools/readdb.h
License
mpiBLAST version 1.5.0-PIO is licensed to the public under the terms of:
The GNU Public License (GPL) version 2
Here is a copy of the license included within every file distributed with mpiBLAST.
This file is part of mpiBLAST.
mpiBLAST is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version of the GNU General Public License.
Accordingly, mpiBLAST is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with mpiBLAST. If not, see .
(17) MUMMER
MUMmer patches and Artistic license.
To: debian-mentors@lists.debian.org
Cc: debian-med@lists.debian.org
Subject: Re: MUMmer patches and Artistic license.
From: Charles Plessy
Date: Sat, 4 Jul 2009 21:06:42 +0900
Message-id: <20090704120642.GH6047@kunpuu.plessy.org>
Mail-followup-to: debian-mentors@lists.debian.org, debian-med@lists.debian.org
In-reply-to: <20090702160647.GA9798@an3as.eu>
References: <20090702160647.GA9798@an3as.eu>
Dear Debian mentors,
we have a patch in the Debian package mummer for which we lost origin and
detailed description. I would like to forward it upstream, but I would prefer
to know what it does before ;) Would somebody have a few minutes to throw an
eye on it? It is in our SVN, and here is a copy:
http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
diff -urbN src/tigr.orig/annotate.cc src/tigr/annotate.cc
--- ./src/tigr.orig/annotate.cc 2007-07-13 19:06:58.000000000 +0200
+++ ./src/tigr/annotate.cc 2007-11-07 21:47:03.000000000 +0100
@@ -10,6 +10,7 @@
*/
#include "tigrinc.hh"
+#include
#define FIELD_LEN 20
#define MAX_ALIGN 10000
@@ -138,19 +139,19 @@
// Print the alignment between strings A [1 .. M] and B [1 .. N] .
{
- static int D [MAX_ALIGN] [MAX_ALIGN];
- static char Op [MAX_ALIGN] [MAX_ALIGN];
- static char Show_A [2 * MAX_ALIGN];
- static char Show_B [2 * MAX_ALIGN];
+ int **D, *D_buf;
+ char **Op, *Op_buf;
+ char *Show_A;
+ char *Show_B;
int Errors, Tmp;
long int i, j, Ct;
- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
- {
- printf ("\n *** Too long ***\n\n");
- fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
- return;
- }
+ assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
+ D = &D_buf ;
+ assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
+ Op = &Op_buf ;
+ assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
+ assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
D [0] [0] = 0;
Op [0] [0] = 'a';
@@ -229,5 +230,10 @@
putchar ('\n');
Ct -= WIDTH;
} while (Ct > 0);
+
+ free ( D_buf ) ;
+ free ( Op_buf ) ;
+ free ( Show_A ) ;
+ free ( Show_B ) ;
return;
}
There is a bit of background on our mailing lists, but it is really parcellar…
> http://lists.debian.org/debian-med/2007/11/msg00045.html
> http://lists.debian.org/debian-devel/2005/06/msg00037.html
The take-home message is of course: DEP3 is good for you!
http://dep.debian.net/deps/dep3/
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Reply to:
debian-med@lists.debian.org
Charles Plessy (on-list)
Charles Plessy (off-list)
Follow-Ups:
Re: MUMmer patches and Artistic license.
From: "Nelson A. de Oliveira"
Re: MUMmer patches and Artistic license.
From: "Boyd Stephen Smith Jr."
References:
Re: MUMmer patches and Artistic license.
From: Andreas Tille
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(18) SOAPdenovo
Copyright: 2008-2010 BGI-Shenzhen
License: GPL-3+
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On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Files: debian/*
Copyright: 2012 Olivier Sallou
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
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This package is distributed in the hope that it will be useful,
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You should have received a copy of the GNU General Public License
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.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
(19) Velvet
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12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
(20) CD-HIT
Copyright: © 2009-2011 Weizhong Li License: GPL-2 Files: cdhit-user-guide.pdf Copyright: © 2009-2011 Weizhong Li License: GPL-2 Comment: LaTeX source for documentation will be included in future release The author provided the source for the documentation in an archive sended in CC to the Debian Med mailing list. The content is stored in the source package in debian/doc-source for the moment. . Date: Wed, 21 Dec 2011 14:23:00 -0800 From: Weizhong Li To: Andreas Tille CC: Debian Med Project List Subject: Re: Packaging of cd-hit for Debian . Andreas, The attached is the LaTex source. This is not currently included in the cd-hit release yet. But in the future, we consider to have the LaTex file packaged into cd-hit release. Thanks a lot, let me know if anything is needed. Weizhong License: GPL-2 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. Files: debian/* Copyright: © 2011 Andreas Tille License: Same as cd-hit itself (GPL-2) On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'.
(21) RAPIDminer
1. Preamble
2. As the provider of this website, we are obliged by law to inform you of the purpose, scope and nature of the collection and use of your personal data. Below is a decription of the way we collect, process and use your data. For further questions, you may contact us at any time.
Your confidence is important to us. Our highest priority is the protection of your personal data. We only use them them as you may expect it from us. Compliance with the relevant statutory data protection regulations is therefore natural for us.
As far as the applicable law requires your explicit consent, we will ask you for it by displaying this declaration. We will log your consent. You can store, retrieve and print the content of your consent at any time.
2. Definitions
Personal data is any information concerning the personal or material circumstances of an identified or identifiable natural person (data subject).
Affiliated companies are those in which the Rapid-I GmbH is involved and which are either obliged to follow this Privacy Policy or are bound to guidelines that grant an officially certified protection, e.g. by joining the Safe Harbor program.
3. Automatically received data
So that the pages can be displayed correctly in your browser and we can send the requested content to you, your IP address is collected and stored. Usually an IP address is currently assigned dynamically. This address changes regularly, so we ourselves cannot make out any personal connection through this IP address. In individual cases (e.g. static IP addresses) a personal reference would be theoretically possible. But as a supplier, we will not and also don’t have any interest in making any personal reference.
Specifically, for each access through your device the following data is stored and used: your IP address, browser type, language setting for the browser, operating system, referring URL, name of the file, date and time of the call, amount of data transferred and report on the success of the call.
Your IP address will be reduced by the last octet immediately after your use and then stored only in this anonymous form. Personal reference is it no longer producible and also not intended.
4. Nature, scope and purpose of collection and use
We make every effort to orient our service to your requirements. The use of our website is therefore entirely possible without prior application or registration. All information about personal data are given to us on a strictly voluntary basis.
Depending on which of our services you wish to use, we store, process and use your personal information. The required mandatory fields are marked with an asterisk (*).
The purpose of the collection, processing and usage is to create a safe, comfortable, reliable and user-friendly user experience. We also use your information for marketing and direct marketing purposes. For other purposes, your data will not be used.
a) Interactive services
As interactive services we understand these services for which you provide content to us as users.
aa) Newsletter, Mailing Lists
If you want to subscribe to our newsletter or our mailing list, we need your e-mail address and your name to send the message to you and to address you. You will receive a check-mail to confirm your free subscription. Only when you follow the link in this e-mail, you will be registered in the newsletter or mailing list.
bb) Contact form
If you use our contact form, we will store and use your e-mail address and the accompanying message to respond to your request.
cc) Registration information
The given information upon registration, we need to help you create an account for your selected service.
Your chosen display name is used to assign an action with communicative character to you and to make that public to other users. Behind the display name of each user, you can find information about the respective users, e.g. which products they offered, how they were rated and also to contact the user.
dd) User account maintenance
During your account maintenance, we save and use further information about you.
This includes your name, address, post office box, telephone number, professional status, company name, department, whether you are buying as a home or business customer, headquarters, VAT, banking and payment data, your chosen invoice number, your products and its description, the corresponding invoices sent to you and from you, if you are supplier, associated licenses and license keys and your bookmarks to product detail pages. This information is visible only to you. You can modify the data by yourself in your user account, or delete it. Required Fields are marked with the asterisk (*).
Other content, such as comments, forum posts, product reviews, we also store. These are visible for other users in connection with your display name. When you send a message with the contact form of a user, we also transmit your registered email address to him or her.
b) Applications
We are also delighted if you join us. Your applications are sent directly to the Human Resources Department by the e-mail address office@rapid-i.com and will of course be treated confidentially. Please see our information on communication by e-mail below on this page. You can of course also send your application by post. Please use the address given in the imprint with the identifier "Human Resources".
c) Transfer
We provide the above information to the relevant authorities within our company, our affiliated companies and appropriate externals to meet our own business purposes, in particular but not only the maintenance of client relationships. We transfer the necessary data to our affiliated companies for sending you marketing and sales materials via electronic, postal or telephonic mail. Our employees and external service providers are bound to secrecy and were advised of the need for the protection of personal data (data confidentiality).
When you order something in our shop, we need to disclose the information to the provider of the ordered services, if he is different from us, in order to fulfill the contractual obligations. The same goes for your e-mail address in the event that you contact another user via the contact form in his account.
We reserve the right to disclose or to pass your information to defend against or enforce any legal claims within court proceedings or its preparation.
A transmission that is not included in these embodiments is not performed. Without your consent or a legal permission, no data is passed. In particular, no personal data will be sold to third parties or marketed in other ways.
d) Technical and organizational measures
We protect your data in technical and organizational expertise from unauthorized access, seizure and any other third-party intervention.
At regular intervals within the legal time, we erase or block all personal data.
We remind you that your personal data is not protected effectively when you disclose your password intentionally or unintentionally to third parties.
5. Cookies
Our websites use cookies. These are small text files stored by your browser on your computer or other devices.
We analyze what pages users have visited most, for what terms they looked, etc. ("web tracking"). In addition, this way, our offer becomes more effective, user-friendly and safe, by e.g. saving you to reenter your password again on every visit or by assigning your orders in your shopping cart. Cookies do no harm to your computer and do not contain viruses.
We only use "session cookies". These cookies are deleted at the end of the session. You can configure your browser so that the use of cookies is done automatically, is sought in each individual case or is completely excluded. Of course, you can even delete cookies from your browser again, and prevent or limit the analysis of your behavior doing so.
We accept, if you don’t want to use cookies. Note, however, that the functionality of our website may then be restricted.
We note that other service providers that can be accessed via links on our site, possibly also use cookies. We have no influence on this process. Therefore, please read the privacy policies of other Web site operators attentively.
6. Google Analytics
The entire website uses Google Analytics, a web analytics service provided by Google Inc. ("Google"). Google Analytics uses "cookies". These are small text files that are stored on your computer to help the website analyze how users habit on the website. The information generated by the cookie about your use of this site are usually sent to a server of Google in the U.S. and stored there.
We expanded Google Analytics with the code "gat._anonymizeIp ();" to enable an IP masking in our administrator console. This means your IP address will be anonymized by deleting the last octet. Only afterwards, it will be sent within Member States of the European Union or other parties to the Agreement on the European Economic Area. Only in exceptional cases, the full IP address is sent to a Google server in the USA and will be shortened there.
On our behalf, Google will use this information to evaluate your use of the website, to compile reports on website activity and to provide other website and internet related services to us.
The IP addresses collected through Google Analytics are not being merged with other data held by Google.
You can prevent the storage of cookies by selecting the appropriate settings on your browser. However, doing so might limit use of certain features of the website.
You can also prevent the recording through the Google Analytics cookie, the transmission of the respective data and its processing through Google by downloading and installing a browser-plug-in, offered by Google.
The current link is: http://tools.google.com/dlpage/gaoptout?hl=de.
7. Facebook Plug-Ins (e.g. like-button)
On our website are plug-ins of the social network "Facebook," Facebook, Inc., 1601 S. California Ave, Palo Alto, California 94304, Phone:. 650-543-4800, fax: 650-543-4801, http://www.facebook.com integrated. The Facebook plug-ins are marked with the “Facebook-logo” or the Facebook "Like-button” ("Like").
When you visit our site, the plug-in establishes a direct connection between your browser and the Facebook-server. Facebook gets therefore the information that you have visited our site with your IP address. With the distributed cookie, Facebook can identify the other websites with a Facebook social-plug-in integrated you have visited.
We point out that we, as website owners, do not have any knowledge of the content of the collected data and its use by Facebook. We neither have access to the data, Facebook collects independently and for itself.
If you click on the Facebook "Like-button” while you are logged in to your Facebook account, you can link the content of our sites on your Facebook profile. This option is also available if you sign up immediately after clicking the "Like-button" to then log into your Facebook profile.
If you do not wish that Facebook can assign your visit on our site to your Facebook user account, please log out from your Facebook account and delete the cookies delivered by Facebook. We emphasize that you have the option to install a tool that prevents the calling of the Facebook social plug-ins.
8. Twitter Plug-Ins (tweet-function)
On our website you will also have the opportunity to use the functions of the service Twitter. It is published on our web site, but offered by Twitter, Inc., 795 Folsom St., Suite 600, San Francisco, CA 94107, USA. The Twitter-Services are marked with the "Twitter-sign," the “Twitter logo” or the "Tweet and Retweet buttons".
When you visit our site, the plug-in establishes a direct connection between your browser and the Twitter-server. Twitter gets therefore the information that you have visited our site with your IP address. With the distributed cookie, Twitter can identify the other websites with a Twitter social-plug-in integrated you have visited.
We point out that we, as website owners, do not have any knowledge of the content of the collected data and its use by Twitter. We neither have access to the data, Twitter collects independently and for itself.
If you click on the “Tweet” or “Retweet”-Button while you are logged in to your Twitter account, you can link the content of our sites on your Twitter profile. This option is also available if you sign up immediately on the prompt to then log into your Twitter profile.
If you do not wish that Twitter can assign your visit on our site to your Twitter user account, please log out from your Twitter account and delete the cookies delivered by Twitter. We emphasize that you have the option to install a tool that prevents the calling of the Twitter social plug-ins.
9. YouTube
On our website you will also have the opportunity to use the functions of the service YouTube. These are published on our web site, but offered by YouTube, LLC, 901 Cherry Ave, San Bruno, CA 94066, USA Phone: +1 650-253-0001-253-0000, Fax: +1 650-253-0001. The YouTube services are identifiable by the "YouTube-sign", the “YouTube logo” or the embedded videos on websites.
When you visit our site, the plug-in establishes a direct connection between your browser and the YouTube-server. YouTube gets therefore the information that you have visited our site with your IP address. With the distributed cookie, YouTube can identify the other websites with a YouTube social-plug-in integrated you have visited.
We point out that we, as website owners, do not have any knowledge of the content of the collected data and its use by YouTube. We neither have access to the data, YouTube collects independently and for itself.
If you do not wish that YouTube can assign your visit on our site to your YouTube user account, please log out from your YouTube account and delete the cookies delivered by YouTube.
10. Lockerz Share
On our website you will also have the opportunity to share our websites with different persons from your community. You can therefore use the "share"-function of Lockerz Inc. ("Lockerz"), 100 South King Street use, Sixth Floor, Seattle, WA 98104, USA. Please recognize the function by the green “Lockerz-icon” or the “Lockerz-logo”.
When you visit our site, the plug-in establishes a direct connection between your browser and the Lockerz-server. Lockerz gets therefore the information that you have visited our site with your IP address. With the distributed cookie, Lockerz can identify the other websites with a Lockerz social-plug-in integrated you have visited.
We point out that we, as website owners, do not have any knowledge of the content of the collected data and its real use by Lockerz. We neither have access to the data, Lockerz collects independently and for itself.
If you do not wish that Lockerz can assign your visit on our site to your Lockerz user account, please log out from your Lockerz account and delete the cookies delivered by Lockerz.
11. Links
We expressly point out that we have no control over compliance with the privacy and security provisions of other website owners. We therefore ask you to read the specific privacy policies carefully. This privacy statement applies only to those operated by the Rapid-I GmbH website.
12. Youth protection
Our websites and the information and services provided thereon are not intended for minors and people who are incapable of contracting.
From our side, no data of individuals is collected, processed or used who are limited in legal capacity or are legally incapacitated, if the consent of the legal representative is absent.
If this happens by unintentionally, we will immediately and permanently delete these data. We are grateful for your assistance in the implementation.
13. Contact
We are open to your questions, suggestions or complaints.
If there is any question left about how your personal data is treated, you want to exercise your right of information or you want to revoke your consent in the collection, storage or use of you personal data, please feel free to contact our Privacy Officer at
Rapid-I GmbH
Privacy Officer
Stockumer Straße 475
D- 44227 Dortmund
Germany
E-Mail: dataprotection@rapid-i.com.
14. Your rights
You may request to see or change any of your Personal Data in your account by contacting us at the e-mail address below.
You may also request that your Personal Data is no loger used for future marketing purposes by contacting us at the e-mail address below.
You can object to the use of data with effect for the future and withdraw your consent with effect for the future. Please send us an e-mail with the resepctive content to dataprotection@rapid-i.com.
15. Communication
Be aware that any communication over the website or through other online instruments is basically unencrypted, unless you an activated security certificate in your browser address bar.
The same applies for e-mails. This type of communication can have security gaps, in particular, there is a theoretical possibility that the messages be read by unauthorized third parties or even changed. If you wish another type of communication, please let us know beforehand.
16. Subject to alteration
We are constantly working to improve the safety and protection of your data and will update this statement as appropriate with the implementation of new industry-standard security terchnologies.
The English version of this declaration serves only for your information shall not suggest that a different legislation may be applicable in addition to the German. In the case of inconsistencies between the German and the English version, the German version shall prevail.
As of: December 2012
(22) MERCI
The MEME Suite
Motif-based sequence analysis tools
MEME Suite
Authors: Timothy L. Bailey, William Noble
Copyright (c) 1994-2009 The Regents of the University of
California. All Rights Reserved.
Permission to use, copy, modify, and distribute any part
of this software for educational, research and non-profit
purposes, without fee, and without a written agreement is
hereby granted, provided that the above copyright notice,
this paragraph and the following three paragraphs appear in
all copies.
Those desiring to incorporate this software into commercial
products or use for commercial purposes should contact the
Technology Transfer Office, University of California, San
Diego, 9500 Gilman Drive, La Jolla, California, 92093-0910,
Phone: (858) 534-5815.
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE
TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR
CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT
OF THE USE OF THIS SOFTWARE, EVEN IF THE UNIVERSITY OF
CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGE.
THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND
THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE
MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND
EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESSED OR
IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR
THAT THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT,
TRADEMARK OR OTHER RIGHTS.
(24) ChemAxon
Academic License conditions
Our free Academic License program aims to give schools and universities the basic tools to develop interactive chemistry teaching resources and advanced tools to enable students and staff to perform original research from within a single platform. Under the program ChemAxon tools, forum support and access to upgrades are available at no charge. Two major types of academic licenses are available: Academic License for Teaching and Academic License for Research. Our package is heavily used around the globe.
How to obtain and maintain a free ChemAxon Academic License?
First you have to log in to our website. If you do not have a user name yet please register yourself.
Read the general conditions and apply for the free license if you think you will fulfill our requirements.
Complete the application and submit.
Your application will be reviewed. We may need additional details during the acceptance process.
Once your application is accepted you can download your license from the My Licenses page.
You must maintain the accuracy of your application. You will need to amend your application if you change or introduce new software use. You will also need to amend your application to inform of implementations or articles generated with data from these tools. To review or amend your application please log in and revisit your application page.
To access the software you should visit this download page and select the software required.
If you have any questions about how to apply for, maintain or access software provided under the Academic License conditions please visit our Academic License support forum.
Academic Research or Teaching License?
Common conditions: Both licenses are valid for two years; they are assigned to named individuals. The license keys – either for research or for teaching – cannot be transferred beyond individuals and groups identified here.
Differences:
Academic Research License: The license is granted for research purposes and the license keys provided are issued to named individuals, the license cannot be distributed. The term of the license is two years, subsequent licenses will be provided if publications can be demonstrated and ChemAxon is correctly cited. Please note that you cannot share this license to carry out research in team or to build a database!
Academic Teaching License: The license is granted for teaching purposes and the license keys provided can be distributed to current members of the department stated in the application. The term of the license is two years which can be extended anytime as long as the license holder teaches.
General conditions of offer
The Academic License is only available to academic organisations.
ChemAxon makes no charge for the provided software offered within the Academic License.
ChemAxon makes no charge for software upgrades or support provided via the Technical Support Forum for software provided within the Academic License.
With the exception of fees related to tuition neither the academic organisation, commercial or academic partners nor any of its employees will receive funds or payments in kind related to the performance of the provided software.
No products, applications, services or any other delivery of software performance which contains the provided software are allowed without the written permission of ChemAxon.
All implementations of provided software should (when possible) credit ChemAxon by placing a logo (image here) with a link to http://www.chemaxon.com, on all the relevant pages or sections of the implementation where the software is providing content.
Any publications or presentations based upon implementations or data generated by provided software must cite ChemAxon. For specific citation information please see our details located here.
Applicants and license holders must remain familiar with the conditions of the Academic License and maintain the accuracy of their applications according to the requested information and respond to requests to confirm the accuracy of application details. For a history of all changes to these conditions please visit Conditions history
ChemAxon’s Academic License is a community driven effort, licensees should, whenever possible, make efforts to support other ChemAxon users through contributing code to the “Contribute” thread of the Technical Support Forum and through offering advice to other ChemAxon users on the Technical Support Forum.
ChemAxon reserves the right to alter the conditions of the Academic License at any time. Any changes to these conditions will be posted to the appropriate section of the Technical Support Forum.
If you have any questions on the Academic License conditions or any other comments please visit our Academic License support forum.
(24) FILTERiT
Site Licensing for FILTERiT4.6
Thank you for your interest in site licensing FILTERiT.
The site licensing program starts from 10 units or more. You will receive 10 % off for an order between 10 and 19 units, 20 % off between 20 and 29 units, 30 % off between 30 and 39 units, 40 % off between 40 and 49 units, and finally 50 % off for 50 units or more. Please see chart below.
CODE
PRODUCT NAME
UNIT PRICE
CS-002-10
FILTERiT4.6/10-19 units
$116.10 per unit
CS-002-20
FILTERiT4.6/20-29 units
$103.20 per unit
CS-002-30
FILTERiT4.6/30-39 units
$90.30 per unit
CS-002-40
FILTERiT4.6/40-49 units
$77.40 per unit
CS-002-50
FILTERiT4.6/50 units or more
$64.50 per unit
Payment Methods
We accept the following payment options for site licensing.
-credit card (MC, VISA, AMEX)
-wire transfer
You can order by e-mailing to orders@cvalley.com
Your order should contain the following:
1) Company name
2) Contact person
3) Address(steet address,city,state,zip code)
4) Country if not U.S.
5) Phone number
6) Fax number
7) E-mail address
8) Name of product(s) you wish to order
9) Number of units(must be 10 or more)
10) Form of payment
Distributed by CValley, Inc.
18552 MacArthur Blvd. Suite 345
Irvine, CA 92612
Email: info@cvalley.com
(25) PADEL
Copyright (C) 2013 by Francisco de Juan
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
(26) clustalw/x
Licensing ClustalW and ClustalX Date:29 November 2007 The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson and Toby Gibson The binaries and source code are made available and can be distributed subject to the following conditions: Users are free to redistribute ClustalW or ClustalX in it's unmodified form as long as it is not for commercial gain. Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at gibson@embl.de If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at clustalw@ucd.ie where they will be considered for inclusion in future releases. Frequently asked questions about Clustal licensing? --------------------------------------------------- 1. Do I have to pay to use ClustalW or ClustalX? No - unless you wish to redistribute Clustal for profit. In this case see question 4. 2. Can I redistribute the Clustal binaries and source code? Yes. We have always wanted to see Clustal have as wide a userbase and distribution network as possible and are happy to see other sites host copies of the official Clustal code. 3. Can I make changes to the source code? You can make changes for your own purposes but you should not redistribute the changed code. 4. I want to include ClustalW/ClustalX in a commercial application who should I contact? Toby Gibson at gibson@embl.de (also cc des.higgins@ucd.ie) 5. There is no Clustal distribution for platform X. I have changed the code in order to compile Clustal on this platform. Can I redistribute it? Ideally you should send us a copy of your source code changes as well as a binary. We will include it in our contributed binaries section on our FTP site along with an acknowledgement of your contribution.
(27) Blast
1 PUBLIC DOMAIN NOTICE
2 National Center for Biotechnology Information
3
4 This software/database is a "United States Government Work" under the
5 terms of the United States Copyright Act. It was written as part of
6 the author's official duties as a United States Government employee and
7 thus cannot be copyrighted. This software/database is freely available
8 to the public for use. The National Library of Medicine and the U.S.
9 Government have not placed any restriction on its use or reproduction.
10
11 Although all reasonable efforts have been taken to ensure the accuracy
12 and reliability of the software and data, the NLM and the U.S.
13 Government do not and cannot warrant the performance or results that
14 may be obtained by using this software or data. The NLM and the U.S.
15 Government disclaim all warranties, express or implied, including
16 warranties of performance, merchantability or fitness for any particul Purpose.Please cite the author in any work or product based on this material.
(28) Blast+
1 PUBLIC DOMAIN NOTICE
2 National Center for Biotechnology Information
3
4 This software/database is a "United States Government Work" under the
5 terms of the United States Copyright Act. It was written as part of
6 the author's official duties as a United States Government employee and
7 thus cannot be copyrighted. This software/database is freely available
8 to the public for use. The National Library of Medicine and the U.S.
9 Government have not placed any restriction on its use or reproduction.
10
11 Although all reasonable efforts have been taken to ensure the accuracy
12 and reliability of the software and data, the NLM and the U.S.
13 Government do not and cannot warrant the performance or results that
14 may be obtained by using this software or data. The NLM and the U.S.
15 Government disclaim all warranties, express or implied, including
16 warranties of performance, merchantability or fitness for any particul Purpose.Please cite the author in any work or product based on this material.
(29) MUSCLE
MUSCLE is public domain software
The MUSCLE software, including object and source code and documentation, is hereby donated to the public domain.
Disclaimer of warranty
THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
(30) Autodock/AutoDock Vina/auto dock tools/auto grid/autodock-CADD/mglutil/ NAMD, PDB2PQR, APBS, MGLToos
AutoDock 4 Beta Release
by gillet — last modified 2006-09-27 16:22
Release Note for AutoDock 4
AutoDock 4 is now available on a limited basis for beta testing. A selected number of users will be given a license for AutoDock4 beta.
In order to be considered for a beta license, please send e-mail to Prof. Arthur Olson (olson@scripps.edu), stating your prior experience with AutoDock and your willingness to provide user feedback during the beta test period. If approved, you will then be sent the license to complete and return. We will consider licenses for commercial companies for evaluation purposes only.
Once the beta test period is over, AutoDock 4.0 will become generally available.
What's new?
AutoDock 4.0 beta not only is it faster than earlier versions, it allows sidechains in the macromolecule to be flexible. As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.
AutoDock 4.0 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibiton constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.
AutoDock 4.0's search methods now include the optimization library, ACRO, from Bill Hart at Sandia National Labs. We have added some new features to our existing evolutionary methods. We still provide the Monte Carlo simulated annealing (SA) method of 2.4 and earlier. The Lamarckian Genetic Algorithm (LGA) is a big improvement on the Genetic Algorithm, and both genetic methods are much more efficient and robust than SA.
(31) MAAP
MAAP is a a custom archive/collection of important New York locations in African-American history. The collection features rich historical maps
and an award winning interface for browsing these maps.
The MAAP administrative interface is built using Turbogears. The production
site (maap.columbia.edu) is published statically based from a snapshot of the
administrative site.
MAAP was developed at the Columbia Center for New Media Teaching and Learning
in partnership with the JPMorgan Chase Foundation, Teachers College and Curriculum Concepts International.
MAAP comes bundled with several other free open-source software as
dependencies, which come with other licenses (compatible with the GPL).
Copyright (C) 2010 Columbia Center for New Media Teaching and Learning
ccnmtl@columbia.edu
Authors:
Jonah Bossewitch jonah@ccnmtl.columbia.edu
Schuyler Duveen sky@columbia.edu
Maurice Matiz maurice@columbia.edu
Liz Day ed2198@columbia.edu
John Frankfurt johnfrankfurt@mac.com
Mark Phillipson mlp55@columbia.edu
Frank Moretti fmoretti@columbia.edu
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This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
http://www.gnu.org/licenses/gpl.html
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(32) DESMOND
DESMOND LICENSE AGREEMENT FOR NON-COMMERCIAL RESEARCH
1. License Grant. Subject to the terms and conditions of this license agreement (the "Agreement"), D. E. Shaw Research, LLC ("DESRES") grants to LICENSEE a limited, royalty-free license, on a non-exclusive, non-transferable, non-assignable, and non-sublicensable basis, to install and use for non-commercial research (as defined below) the molecular dynamics software program known as Desmond Version 2 (including any version of such program whose version number begins with "2.") and any associated documentation (any such documentation and any such version collectively referred to herein as the "SOFTWARE"). The SOFTWARE may be accessed, held, or otherwise used only with a valid license and this Agreement confers a valid license only to (a) academic or other not-for-profit research entities and (b) individuals who are affiliated with such entities, in each case (a) and (b), provided that such entities and/or individuals use the SOFTWARE exclusively for non-commercial research purposes. 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(33) GROMACS
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TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other program which contains a notice placed by the copyright holder or other authorized party saying it may be distributed under the terms of this Lesser General Public License (also called "this License"). Each licensee is addressed as "you".
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1. You may copy and distribute verbatim copies of the Library's complete source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and distribute a copy of this License along with the Library.
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(For example, a function in a library to compute square roots has a purpose that is entirely well-defined independent of the application. Therefore, Subsection 2d requires that any application-supplied function or table used by this function must be optional: if the application does not supply it, the square root function must still compute square roots.)
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NO WARRANTY
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest possible use to the public, we recommend making it free software that everyone can redistribute and change. You can do so by permitting redistribution under these terms (or, alternatively, under the terms of the ordinary General Public License).
To apply these terms, attach the following notices to the library. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
one line to give the library's name and an idea of what it does.
Copyright (C) year name of author
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the library, if necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in
the library `Frob' (a library for tweaking knobs) written
by James Random Hacker.
signature of Ty Coon, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!
(34) PyMOL
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(37) UCSF Chimera
Licensing
UCSF Chimera is licensed for noncommercial use at no cost by the Regents of the University of California. You must agree to the terms and conditions of use as specified in the license agreement before you will be permitted to download Chimera (preview the agreement).
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(38) Avogadro
GNU Free Documentation License
Version 1.3, 3 November 2008
Copyright © 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
0. PREAMBLE
The purpose of this License is to make a manual, textbook, or other functional and useful document "free" in the sense of freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications made by others.
This License is a kind of "copyleft", which means that derivative works of the document must themselves be free in the same sense. It complements the GNU General Public License, which is a copyleft license designed for free software.
We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference.
1. APPLICABILITY AND DEFINITIONS
This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration, to use that work under the conditions stated herein. The "Document", below, refers to any such manual or work. Any member of the public is a licensee, and is addressed as "you". You accept the license if you copy, modify or distribute the work in a way requiring permission under copyright law.
A "Modified Version" of the Document means any work containing the Document or a portion of it, either copied verbatim, or with modifications and/or translated into another language.
A "Secondary Section" is a named appendix or a front-matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document's overall subject (or to related matters) and contains nothing that could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of legal, commercial, philosophical, ethical or political position regarding them.
The "Invariant Sections" are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any Invariant Sections then there are none.
The "Cover Texts" are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that says that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may be at most 25 words.
A "Transparent" copy of the Document means a machine-readable copy, represented in a format whose specification is available to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not "Transparent" is called "Opaque".
Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input format, SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally available, and the machine-generated HTML, PostScript or PDF produced by some word processors for output purposes only.
The "Title Page" means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material this License requires to appear in the title page. For works in formats which do not have any title page as such, "Title Page" means the text near the most prominent appearance of the work's title, preceding the beginning of the body of the text.
The "publisher" means any person or entity that distributes copies of the Document to the public.
A section "Entitled XYZ" means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as "Acknowledgements", "Dedications", "Endorsements", or "History".) To "Preserve the Title" of such a section when you modify the Document means that it remains a section "Entitled XYZ" according to this definition.
The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.
2. VERBATIM COPYING
You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough number of copies you must also follow the conditions in section 3.
You may also lend copies, under the same conditions stated above, and you may publicly display copies.
3. COPYING IN QUANTITY
If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the Document's license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects.
If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably) on the actual cover, and continue the rest onto adjacent pages.
If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-readable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from which the general network-using public has access to download using public-standard network protocols a complete Transparent copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public.
It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document.
4. MODIFICATIONS
You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the Modified Version:
• A. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous versions (which should, if there were any, be listed in the History section of the Document). You may use the same title as a previous version if the original publisher of that version gives permission.
• B. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the Modified Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has fewer than five), unless they release you from this requirement.
• C. State on the Title page the name of the publisher of the Modified Version, as the publisher.
• D. Preserve all the copyright notices of the Document.
• E. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices.
• F. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version under the terms of this License, in the form shown in the Addendum below.
• G. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document's license notice.
• H. Include an unaltered copy of this License.
• I. Preserve the section Entitled "History", Preserve its Title, and add to it an item stating at least the title, year, new authors, and publisher of the Modified Version as given on the Title Page. If there is no section Entitled "History" in the Document, create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the Modified Version as stated in the previous sentence.
• J. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and likewise the network locations given in the Document for previous versions it was based on. These may be placed in the "History" section. You may omit a network location for a work that was published at least four years before the Document itself, or if the original publisher of the version it refers to gives permission.
• K. For any section Entitled "Acknowledgements" or "Dedications", Preserve the Title of the section, and preserve in the section all the substance and tone of each of the contributor acknowledgements and/or dedications given therein.
• L. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the equivalent are not considered part of the section titles.
• M. Delete any section Entitled "Endorsements". Such a section may not be included in the Modified Version.
• N. Do not retitle any existing section to be Entitled "Endorsements" or to conflict in title with any Invariant Section.
• O. Preserve any Warranty Disclaimers.
If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to the list of Invariant Sections in the Modified Version's license notice. These titles must be distinct from any other section titles.
You may add a section Entitled "Endorsements", provided it contains nothing but endorsements of your Modified Version by various parties—for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard.
You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one.
The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version.
5. COMBINING DOCUMENTS
You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.
The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.
In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements".
6. COLLECTIONS OF DOCUMENTS
You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.
You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.
7. AGGREGATION WITH INDEPENDENT WORKS
A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.
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8. TRANSLATION
Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.
If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.
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You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense, or distribute it is void, and will automatically terminate your rights under this License.
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Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, receipt of a copy of some or all of the same material does not give you any rights to use it.
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The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See http://www.gnu.org/copyleft/.
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ADDENDUM: How to use this License for your documents
To use this License in a document you have written, include a copy of the License in the document and put the following copyright and license notices just after the title page:
Copyright (C) YEAR YOUR NAME. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License".
If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the "with … Texts." line with this:
with the Invariant Sections being LIST THEIR TITLES, with the Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit the situation.
If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your choice of free software license, such as the GNU General Public License, to permit their use in free software.
(39) Ligplot+
# Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=4 inherit java-pkg-2 DESCRIPTION="GUI-based version of LIGPLOT" HOMEPAGE="http://www.ebi.ac.uk/thornton-srv/software/LigPlus/" SRC_URI="LigPlus.zip" SLOT="0" LICENSE="ligplot+" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" RDEPEND="virtual/jre" DEPEND="" RESTRICT="fetch" S="${WORKDIR}"/LigPlus QA_PREBUILT="opt/${PN}/.*" pkg_nofetch() { einfo "Please visit" einfo "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html" einfo "download ${A}" einfo "and save in ${DISTDIR}" } src_prepare() { rm -rf lib/*{win,mac} || die } src_install() { insinto /opt/${PN} doins -r lib LigPlus.jar make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\"" }
(40) Scilab
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(41) MOPAC
MOPAC2012 is available free for academic, not-for-profit use. Please complete the following form to request a license key. An email address from a bona-fide academic institution* is required. If you already have a license for MOPAC2009, please download a new executable. Do NOT fill out this form. You can get Request license form at http://openmopac.net/download-c.html .
(42) EMBOSS
EMBOSS License
The AJAX and NUCLEUS libraries are released under the GNU Library General Public Licence.
EMBOSS applications are released under the GNU General Public Licence.
Parsing of ACD files does not constitute a "derived work" and developers are encouraged to do this, for example to write their own GUIs.
For developers who have their own licensing conditions already in effect, there will be an additional way to contribute. The EMBASSY collection can include packages that use the EMBOSS core libraries and interfaces but under their own licensing conditions. They will be bound by the Library GPL of the AJAX and NUCLEUS libraries, but not necessarily by the full GPL.
For more information on how to develop your own EMBOSS applications, contact emboss-bug@emboss.open-bio.org
(43) RepeatMasker
The Open Software License 2.1 (OSL-2.1)
(Note: This license has been superseded by the Open Software License, version 3.0)
Open Software License v. 2.1
This Open Software License (the "License") applies to any original work of authorship (the "Original Work") whose owner (the "Licensor") has placed the following notice immediately following the copyright notice for the Original Work:
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2) Grant of Patent License. Licensor hereby grants You a world-wide, royalty-free, non-exclusive, perpetual, sublicenseable license, under patent claims owned or controlled by the Licensor that are embodied in the Original Work as furnished by the Licensor, to make, use, sell and offer for sale the Original Work and Derivative Works.
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7) Warranty of Provenance and Disclaimer of Warranty. Licensor warrants that the copyright in and to the Original Work and the patent rights granted herein by Licensor are owned by the Licensor or are sublicensed to You under the terms of this License with the permission of the contributor(s) of those copyrights and patent rights. Except as expressly stated in the immediately proceeding sentence, the Original Work is provided under this License on an "AS IS" BASIS and WITHOUT WARRANTY, either express or implied, including, without limitation, the warranties of NON-INFRINGEMENT, MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF THE ORIGINAL WORK IS WITH YOU. This DISCLAIMER OF WARRANTY constitutes an essential part of this License. No license to Original Work is granted hereunder except under this disclaimer.
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9) Acceptance and Termination. If You distribute copies of the Original Work or a Derivative Work, You must make a reasonable effort under the circumstances to obtain the express assent of recipients to the terms of this License. Nothing else but this License (or another written agreement between Licensor and You) grants You permission to create Derivative Works based upon the Original Work or to exercise any of the rights granted in Section 1 herein, and any attempt to do so except under the terms of this License (or another written agreement between Licensor and You) is expressly prohibited by U.S. copyright law, the equivalent laws of other countries, and by international treaty. Therefore, by exercising any of the rights granted to You in Section 1 herein, You indicate Your acceptance of this License and all of its terms and conditions. This License shall terminate immediately and you may no longer exercise any of the rights granted to You by this License upon Your failure to honor the proviso in Section 1(c) herein.
10) Termination for Patent Action. This License shall terminate automatically and You may no longer exercise any of the rights granted to You by this License as of the date You commence an action, including a cross-claim or counterclaim, against Licensor or any licensee alleging that the Original Work infringes a patent. This termination provision shall not apply for an action alleging patent infringement by combinations of the Original Work with other software or hardware.
11) Jurisdiction, Venue and Governing Law. Any action or suit relating to this License may be brought only in the courts of a jurisdiction wherein the Licensor resides or in which Licensor conducts its primary business, and under the laws of that jurisdiction excluding its conflict-of-law provisions. The application of the United Nations Convention on Contracts for the International Sale of Goods is expressly excluded. Any use of the Original Work outside the scope of this License or after its termination shall be subject to the requirements and penalties of the U.S. Copyright Act, 17 U.S.C. § 101 et seq., the equivalent laws of other countries, and international treaty. This section shall survive the termination of this License.
12) Attorneys Fees. In any action to enforce the terms of this License or seeking damages relating thereto, the prevailing party shall be entitled to recover its costs and expenses, including, without limitation, reasonable attorneys' fees and costs incurred in connection with such action, including any appeal of such action. This section shall survive the termination of this License.
13) Miscellaneous. This License represents the complete agreement concerning the subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable.
14) Definition of "You" in This License. "You" throughout this License, whether in upper or lower case, means an individual or a legal entity exercising rights under, and complying with all of the terms of, this License. For legal entities, "You" includes any entity that controls, is controlled by, or is under common control with you. For purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.
15) Right to Use. You may use the Original Work in all ways not otherwise restricted or conditioned by this License or by law, and Licensor promises not to interfere with or be responsible for such uses by You.
This license is Copyright (C) 2003-2004 Lawrence E. Rosen. All rights reserved. Permission is hereby granted to copy and distribute this license without modification. This license may not be modified without the express written permission of its copyright owner.
(44) PloyPhen
Software
Licensing
The software provided herein is free for academic instruction and research use only. Commercial licenses are available to legal entities, including companies and organizations (both for-profit and non-profit), requiring the software for general commercial use. To obtain a commercial license please, contact us via e-mail.
Disclaimer
This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The code should not be modified and/or redistributed without the permission of the authors.
(45) SIFT
SIFT
SIFT feature detection implementation Copyright (C) 2004, Sebastian Nowozin (nowozin@cs.tu-berlin.de) All rights reserved. There follows a formal license for this software, please read it carefully. Probably the most important part for the user is its restriction to non-commercial use only. The license used the BSD license as template. LICENSE Use of this software and redistribution in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Any redistribution must contain the complete source code, including all modifications. Alternatively, the redistribution may contain a permanent pointer to an Internet address where the full modified source code is available for download free of charge. * The redistributed software contains the following text as prominent notice in the source code and as displayed program output whenever the program is run: "This software is provided for non-commercial use only. The University of British Columbia has applied for a patent on the SIFT algorithm in the United States. Commercial applications of this software may require a license from the University of British Columbia." * Neither the name of the authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. * The redistributed software must retain the above copyright notice, this list of conditions and the following disclaimer. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
(46) GLIMMER
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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1. Definitions.
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"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work.
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You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and
If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.
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9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.
(47) UniPro UGENE
License: This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. If you wish to use Unipro UGENE code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact us (ugene@unipro.ru) for permission. Incorporation into commercial software under non-GPL terms is possible by obtaining a specially licensed version from Unipro. Contact 'ugene@unipro.ru' to arrange licensing terms. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this Unipro UGENE release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. See /usr/share/common-licenses/GPL for the complete text of the GPL Files: src/core/src/document_format/IOLibsUtils.h src/core/src/document_format/ABIFormat.cpp src/core/src/document_format/SCFFormat.cpp Copyright: 1994 Medical Research Council. All rights reserved. License: Permission to use, copy, modify and distribute this software and its documentation for any purpose is hereby granted without fee, provided that this copyright and notice appears in all copies. MRC disclaims all warranties with regard to this software. The File src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h Copyright (C) 1992-2008 Trolltech ASA Released under the terms of GPL (v2 or any later version). (http://labs.trolltech.com/page/Projects/QtScript/Generator) The Files in src/libs_3rdparty/qtbindings_core src/libs_3rdparty/qtbindings_gui src/libs_3rdparty/qtbindings_xml are automatically generated by Qt Script Generator (http://labs.trolltech.com/page/Projects/QtScript/Generator) and have the same license as the API they binds. Therefore, this files are relased under the terms of GPL. The File src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp Copyright (c) 1998 Todd C. Miller Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. The Files in src/plugins_3rdparty/hmm2 HMMER - Biological sequence analysis with profile hidden Markov models Copyright (C) 1992-2003 HHMI/Washington University School of Medicine This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. If you wish to use HMMER code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact me (eddy@genetics.wustl.edu) for permission. Incorporation into commercial software under non-GPL terms is possible by obtaining a specially licensed version from Washington University School of Medicine. Contact Jack Pincus (jhpincus@cris.com) to arrange licensing terms. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this HMMER release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. See /usr/share/common-licenses/GPL for the complete text of the GPL Note: The Files in src/plugins_3rdparty/uhmmer/src/u_spu and src/plugins_3rdparty/uhmmer/src/uhmmsearch_cell.cpp are modified sources from the HMMER-Cell project (ftp://selab.janelia.org/pub/software/hmmer/contrib-2.3.2/HMMerCell_src_02272008.tar.gz) Original Copyright: 2008, International Business Machines Corporation Authors: Kursad Albayraktaroglu, Jizhu Lu This files are released under the terms of GPL (v2 or any later version). The Files in src/plugins_3rdparty/umuscle/src/muscle and src/plugins_3rdparty/umuscle4/src/muscle4 are PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm) The Files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug Copyright (C) 2007-2008 Trolltech ASA. All rights reserved. This file is part of the Qt Script Debug project on Trolltech Labs. This file may be used under the terms of the GNU General Public License version 2.0 as published by the Free Software Foundation and appearing in the file LICENSE.GPL included in the packaging of this file. This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. The Files src/plugins_3rdparty/psipred/src/seq2mtx.cpp src/plugins_3rdparty/psipred/src/sspred_avpred.cpp src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp Copyright (C) 2000 D.T. Jones These files are distributed under the terms of custom GPL-compatible license. See src/plugins_3rdparty/psipred/src/license for details. The Files in src/plugins_3rdparty/primer3/src/primer3_core Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), and Helen Skaletsky All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of the copyright holders nor contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The Files in src/plugins_3rdparty/hmm3/src/hmmer3 (except files in src/plugins_3rdparty/hmm3/src/hmmer3/easel) Copyright (C) 2009 Howard Hughes Medical Institute. Other copyrights also apply. See the src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT file for a full list. HMMER is distributed under the terms of the GNU General Public License (GPLv3). The Files in src/plugins_3rdparty/hmm3/src/hmmer3/easel Copyright (C) 2009 Howard Hughes Medical Institute. Other copyrights also apply. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/COPYRIGHT file for a full list. Easel is distributed under the Janelia Farm Software License, a BSD license. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE file for more details. The Files in src/plugins/biostruct3d_view/src/gl2ps GL2PS, an OpenGL to PostScript Printing Library Copyright (C) 1999-2006 Christophe Geuzaine This program is free software; you can redistribute it and/or modify it under the terms of either: a) the GNU Library General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version; or b) the GL2PS License as published by Christophe Geuzaine, either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See either the GNU Library General Public License or the GL2PS License for more details. The Files in src/plugins_3rdparty/ball/include and src/plugins_3rdparty/ball/source Copyright (C) Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt and others 1996-2009 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
(48) Blast2go
Privacy Policy
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(49) CCP4
CCP4 Licence
COMMERCIAL END USER LICENCE AGREEMENT (CCP4)
Software: PHASER Version: 1.3
This End User Licence Agreement ("Agreement") is a legal agreement between your company the "Licensee" and CAMBRIDGE UNIVERSITY TECHNICAL SERVICES LIMITED ("CUTS") whose registered office is at 16 Mill Lane, Cambridge, CB2 1SB UK.
CUTS is a company wholly owned by the Chancellor, Masters and Scholars of the University of Cambridge which holds title in intellectual property rights including in the Software and carries on trading, business and technology transfer transactions on behalf of the University of Cambridge.
CUTS is the entire legal and beneficial owner and licensor of the Software and is willing to license use of the Software by the Licensee. As a condition precedent to the execution and performance of this Licence, the Licensee (and/or any of its Affiliates, if applicable, the Licensee and its Affiliates collectively referred to as the "Licensee" for the purposes of this Agreement) will have paid up annual fees to the Council for the Central Laboratory of the Research Councils ("CCLRC") for use of software, including the Software which is the subject of the Licence in this Agreement, which has been assembled by the CCLRC with support from the Biotechnology and Biological Sciences Research Council ("BBSRC") of the UK as part of the Collaborative Computational Project Number 4 ("CCP4").
Downloading the Software from its internet publication site (restricted access via user ID and password) at http://www-structmed.cimr.cam.ac.uk/phaser/download.html, installing, or use of the Software by the Licensee indicates the Licensee's agreement to be bound by the terms and conditions of this Agreement. If the Licensee does not agree to these terms and conditions, the Licensee may not download, install or use the Software.
AGREED TERMS
1. DEFINITIONS
1.1 In this Agreement the following words and phrases shall, unless the context otherwise requires, have the following meanings:
Commencement Date means the initial date of download of the Software from its internet publication site by the Licensee;
Derivatives means computer programs in machine readable object code or source code form developed or otherwise acquired by the Licensee which are a modification of, enhancement to, derived from or based upon the Software;
Fee means the annual licence fee payable by the Licensee to the CCLRC;
Intellectual Property Rights means all patents, copyrights, design rights, trade marks, service marks, trade secrets, know-how, database rights and other rights in the nature of intellectual property rights (whether registered or unregistered) and all applications for the same, anywhere in the world;
Parties means CUTS and the Licensee and "Party" shall mean either of them;
Software means the computer program and version listed at the head of this Agreement.
2. GRANT OF LICENCE
2.1 In consideration of the Fee, CUTS hereby grants to the Licensee a non-exclusive, non-transferable, royalty-free licence, commencing on the Commencement Date and for the duration of payment of the Fee, to download, install and use the Software subject to the following terms and conditions:
(a) the Licensee may use the Software solely for its internal use and the Licensee shall not sell, give, disclose, lend, transfer, sublicense or otherwise distribute the Software to any third party, or allow the Software to be accessed over the internet or in any other manner that would allow access to the Software by anyone other than the Licensee's employees (and consultants and contractors provided such use is solely for the Licensee's internal use and subject to the provisions of this Agreement);
(b) the Licensee may create Derivatives solely for its own internal use but shall not distribute the Software or any Derivatives in whole or in part to any third party;
(c) the Software may be installed and used only on computers owned or leased by the Licensee;
(d) the Licensee may copy the Software solely to the extent necessary to exercise this Licence, and for backup, disaster recovery and archival purposes, provided that the Licensee shall retain on all copies of the Software the following copyright notice: � 2000-2005. Cambridge University Technical Services Limited. All rights reserved.
3. INTELLECTUAL PROPERTY RIGHTS
3.1 The Licensee acknowledges that all Intellectual Property Rights in the Software belong and shall belong to CUTS and the Licensee shall have no rights in or to the Software other than the right to use it in accordance with the terms of the Licence in this Agreement.
3.2 Title to and ownership of any portion of the Software incorporated into Derivatives shall at all times remain with CUTS and the Licensee shall not have any title or ownership interest therein.
3.3 Title to and ownership of any portion of Derivatives created by the Licensee and not owned by CUTS pursuant to Clauses 3.1 and 3.2 above shall be held by the Licensee. Nothing contained in this Licence shall be construed to limit CUTS rights to modify or to develop other derivatives of the Software which are similar to or offer the same or similar improvements as any Derivatives developed by the Licensee.
3.4 Error fixes, bug fixes, technical suggestions, comments and suggested improvements to the Software and its code are welcome by the authors of the Software and CUTS, and in agreeing to provide these to the authors or to CUTS the Licensee hereby assigns the Intellectual Property Rights in error fixes, bug fixes, or technical improvements to CUTS which are communicated in any manner or medium to the authors of the Software or CUTS with a reservation of use of those improvements and suggestions by the Licensee subject to the terms and conditions of the Licence in this Agreement.
4. NO MAINTENANCE OR SUPPORT
4.1 CUTS is under no obligation whatsoever to:
(a) provide maintenance or support for the Software; or
(b) notify the Licensee of error fixes, bug fixes, patches, or upgrades to the features, functionality or performance of the Software ("Enhancements") (if any), whether developed by CUTS or third parties. If, in its sole discretion, CUTS makes an Enhancement available to the Licensee and CUTS does not separately enter into a written licence agreement with the Licensee relating to such bug fix, patch or upgrade, then it shall be deemed incorporated into the Software and subject to this Agreement.
5. DISCLAIMER OF WARRANTIES
5.1 CUTS warrants that the Software will conform substantially with its functional specifications. Otherwise the Software is supplied "as is" without warranty of any kind. CUTS, its licensors and its employees:
(a) disclaim any warranties, express or implied, including but not limited to any implied warranties of merchantability, fitness for a particular purpose, title or non-infringement of third party rights;
(b) do not assume any legal liability or responsibility for the accuracy, completeness, or usefulness of the Software;
(c) do not represent that use of the Software will not infringe privately owned rights;
(d) do not warrant that the Software will function uninterrupted, that it is error-free or that any errors will be corrected.
6. LIMITATION OF LIABILITY
6.1 In no event will CUTS or its licensors or its employees be liable to the Licensee for any indirect, incidental, consequential, special or punitive damages of any kind or nature, including but not limited to loss of profits or loss of data, for any reason whatsoever, whether such liability is asserted on the basis of contract, tort (including negligence or strict liability), or otherwise, even if CUTS has been warned of the possibility of such loss or damages. In no event shall CUTS' liability arising from or in connection with this Agreement exceed a sum equivalent to the annual Fee paid by the Licensee to CCLRC for use of the Software.
6.2 The limitations and exclusions in this Agreement shall not apply in respect of claims for personal injury or death caused by the negligence of CUTS, its licensors or its employees or in respect of fraud or fraudulent misrepresentation.
7. INDEMNITY
7.1 The Licensee shall indemnify CUTS, the Software authors, the Software sponsors, and their agents, officers, and employees, against any and all claims, suits, losses, damages, costs, fees, and expenses arising out of or in connection with any claim or threatened claim by any third party relating to or arising from the use of the Software by the Licensee. The Licensee shall pay all costs incurred by CUTS in enforcing this provision.
8. TERM AND TERMINATION
8.1 This Agreement and the Licence granted herein shall come into effect on the Commencement Date and will continue for the duration of payment of the Fee unless terminated by CUTS in accordance with this Agreement. If the Licensee breaches any term of this Agreement, and fails to cure such breach within thirty (30) days of the date of written notice, this Agreement shall immediately terminate. Upon such termination the Licensee shall immediately cease using the Software, return to CUTS or destroy all copies of the Software, and provide CUTS with written certification of the Licensee's compliance with the foregoing. Termination shall not relieve the Licensee from its obligations arising prior to such termination. Notwithstanding any provision of this Agreement to the contrary, Sections 3, 5, 6, 7, 8, 9, 10, 13, 14 and 18 shall survive termination of this Agreement.
9. CONFIDENTIALITY
9.1 The Licensee agrees and undertakes that during the term of the Licence in this Agreement and thereafter it will keep confidential all, and will not use for its own purposes nor without the prior written consent of CUTS disclose to any third party any information of a confidential nature (including trade secrets and information of commercial value) which may become known to the Licensee and which relates to CUTS unless such information is public knowledge or already known to the Licensee at the time of disclosure or subsequently becomes public knowledge other by breach of the Licence in this Agreement or subsequently comes lawfully into the possession of the Licensee from a third party.
10. NO SUBLICENSING AND NO ASSIGNMENT
10.1 The Licensee shall have no right to sub-license or to assign, transfer, charge or deal in any other manner the benefit or burden of the Licence in this Agreement in whole or in part or to allow the Software to become the subject of any charge, lien or encumbrance without the prior written consent of CUTS such consent may be withheld without giving any reasons.
11. WAIVER
11.1 No forbearance or delay by either party in enforcing its rights will prejudice or restrict the rights of that party, and no waiver of any such rights or of any breach of any contractual terms will be deemed to be a waiver of any other right or of any later breach.
12. SEVERABILITY
12.1 If any provision of the Licence in this Agreement is judged to be illegal or unenforceable, the continuation in full force and effect of the remainder of the provisions will not be prejudiced.
13. NO AGENCY OR PARTNERSHIP
13.1 Nothing contained or implied in this Agreement constitutes a Party the partner, agent, or legal representative of another party or of the other Party for any purpose or creates any partnership, agency or trust, and no Party has any authority to bind the other Party in any way.
14. THE CONTRACTS (RIGHTS OF THIRD PARTIES) ACT 1999
14.1 The Contracts (Rights of Third Parties) Act 1999 shall not apply to this Agreement and nothing in this Agreement shall confer or purport to confer on or operate to give any third Party any benefit or any right to enforce any term of this Agreement except as expressly provided in this Agreement.
15. NOTICES
15.1 Any notice to be given under this Agreement shall be in writing and delivered by hand, prepaid registered post or facsimile to a Party at the address set out at the head of this Agreement or to such other address or fax number as any Party may specify in writing to another. Notices are deemed to have been given:
(a) if delivered by hand, at the time of delivery unless delivered after 5pm in the place of receipt or on a non-business day, in which case the notice is deemed to have been given at 9am the next business day;
(b) if sent by registered post from within the United Kingdom, three business days after posting (or seven business days if posted from outside the United Kingdom); and
(c) if sent by facsimile, at the time the facsimile is received shown in the transmission report as the time that the whole facsimile was sent unless received after 5pm in the place of receipt or on a non-business day, in which case the notice is deemed to have been given at 9am the next business day. Any notice served by facsimile transmission shall be confirmed by post.
16. ENTIRE AGREEMENT
16.1 This Agreement constitutes the entire agreement and understanding of the Parties and supersedes all negotiations, understandings or previous agreement between the Parties relating to the subject matter of this Agreement.
17. GOVERNING LAW
17.1 This Agreement and any documents to be entered into pursuant to it shall be governed by and construed in accordance with English law and each Party irrevocably submits to the exclusive jurisdiction of the courts of England over any claim or matter arising under or in connection with this Agreement and the documents entered into pursuant to it.
18. EXPORT CONTROL REGULATIONS
18.1 'Export Control Regulations' means any United Nations trade sanctions or EU or UK legislation or regulation, from time to time in force, which impose arms embargoes or control of export of goods, technology or software.
18.2 The Licensee shall ensure that, in using the Software it shall not and nor shall its employees or consultants or contractors breach or compromise directly of indirectly compliance with any Export Control Regulations.
If you have any questions or feedback concerning the Software, contact University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY UK. Attn: Professor Randy Read, or via email at cimrphaser@lists.cam.ac.uk
(50) Revolution R
LEGAL
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Text last modified November 20, 2008
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(51) Hammer
Cryptogenomicon
The Eddy/Rivas lab and HMMER project: genome sequence analysis
« Graduation day: HMMER3 beta test (3.0b1) release
Computational challenges in large-scale sequencing »
HMMER policy on trademark, copyright, patents, and licensing
April 29th, 2009
There are two ways of spreading light: to be the candle or the mirror that reflects it.
– Edith Wharton, Vesalius in Zante
On April 14, the US Patent and Trademark Office awarded us a trademark on HMMER. This is a good moment to explain how we plan to deal with intellectual property.
HMMER is scientific software, and its methods are described in journal publications. That means that it must be made available in a form that enables any scientist to understand, reproduce, and extend – like any other result of a scientific paper. For software, this is essentially the same as what people mean by “open source”. Our intent is to make HMMER widely and freely available to the entire scientific community as open source code. At the same time, we have to recognize that HMMER is a large, growing, and increasingly valuable codebase, not just a one-off result, so we’re taking steps to make sure we can sustain it as a long term, coherent open source project.
LICENSE
HMMER3 is licensed under the GPLv3 (GNU General Public License, version 3). This means anyone can use it, study it, modify it, and even redistribute it — with the requirement that any modified/redistributed versions must also be licensed under the GPLv3. This explicitly includes both “noncommercial” and “commercial” use (whatever that means, in these days of multibillion dollar research universities and garage biotech startups). People at companies are scientists too, with the same rights and responsibilities regarding results in the scientific literature. The only thing the GPLv3 really blocks is someone forking a derivative copy of HMMER and distributing it under a different license, such as a closed-source proprietary license; to do that, you’d need to negotiate a non-GPL license with us first.
COPYRIGHT
We really don’t expect to negotiate any non-GPL licenses, though. We want to enable many different people to contribute to a single open source HMMER codebase, as a shared codebase for bioinformatics and computational biology. Having a lot of contributors means having a lot of copyrights. Many different copyrights already apply to HMMER, and we plan for even more; negotiating with all those copyright holders to obtain a non-GPL license will be prohibitive (for me, if not for you). It’s relatively easy to get everyone to agree to donate their copyrighted code under license terms compatible with the open source GPLv3, and that’s what we plan to do.
The Howard Hughes Medical Institute (HHMI; my employer) is the main copyright holder. Our terrific Hughes lawyer, Heidi Henning, has negotiated with Washington University (St. Louis USA) and the Medical Research Council Laboratory of Molecular Biology (MRC-LMB; Cambridge UK), my former employers, to transfer their copyrights to HHMI. We also have bits of code from a number of other sources, including Apple, IBM, and some other companies of various sizes, and several individuals in the comp bio community.
TRADEMARK
Did I mention, we want to enable a single open source HMMER codebase? There are several different “HMMERs” out there, some of which have forked HMMER code, some of which say they are independent implementations, and some of which aren’t very clear what they are. I don’t think this confusion around the name is useful for the community, and frankly, I find it somewhat annoying that people are forking rather than working together. (I also disbelieve that it is possible to independently implement HMMER, because there’s so much unpublished trickery in the code; so as far as I’m concerned, either a faux non-open HMMER is getting different and probably wrong answers and making me look bad, or it’s infringing my work and my license and making me mad.) Especially now with the advent of HMMER3, these other “HMMERs” are obsolete, imho.
To help drive cohesion of a single codebase, we have trademarked HMMER. I would now ask anyone who is distributing something called “HMMER” that is not HMMER to change their name to something else, in order not to confuse people. We will soon start “enforcing” the HMMER trademark with some friendly letters, if needed — these letters will be requests to work together on a common codebase. Of course you are still free to use the codebase under the terms of the GPLv3 for whatever you want — just please don’t call modified versions “HMMER”. If you make useful modifications, please consider contributing them back to HMMER instead. We think the “brand recognition” of HMMER is going to help motivate people to cooperate rather than fork.
Part of this plan involves us taking on more responsibility — we are making a commitment to spending time and effort on integrating useful modifications into the HMMER codebase. For example, I’m already making plans with Bjarne Knudsen and CLCbio (Copenhagen, Denmark) to work together to make sure that CLC will be able to integrate the open source version of HMMER3, rather than needing their own version.
PATENTS
We have debated defensively patenting the key innovations in HMMER3, but decided against it. HHMI, to its great credit, is perfectly prepared to file patents solely to defend the intellectual turf of an open source software tool — that is, if we were to be challenged by some commercial patent holder on something, we could fight fire with fire. In the end, though, I feel that software patents on published scientific results are sufficiently controversial and in conflict with the openness required of published scientific results that we decided we didn’t want to go there.
We are prepared to license and incorporate other people’s patented technologies in HMMER3, if necessary. The first example of that is the incorporation of patent-pending technology from Michael Farrar, which I use at the heart of HMMER3′s SIMD vector acceleration code. We licensed that technology nonexclusively from Michael specifically limited to its use in HMMER open source code, and we’ll do that with other future technologies as needed. The “patent clause” of the GPLv3 automatically conveys a nonexclusive license to you, and on through to derivative works. This means that you don’t have to do anything; the GPLv3 is automagically taking care of patent issues, once HHMI and I have done the right licensing up front. This is a big reason why I’m using the GPLv3.
A lot of thought has gone into our positions on HMMER’s intellectual property, thanks especially to discussions with HHMI lawyers and staff (Heidi Henning, Seth Brown, and Joanne Theurich). We think we’ve got this right, for a sustainable long-term plan of open source software development that benefits the whole community. But if you have comments or criticisms, this is a good time to hear them.
Posted in HMMER, Policy on April 29th, 2009 at 10:43 am
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(52) Newbler
# $Id$
## Newbler is distributed as a compiled binary.
Summary: Newbler - De novo assembler for 454 sequence reads
Name: newbler
Version: 2.6
Release: 3
License: Commercial (free for academic use)
Vendor: 454 Life Sciences
Group: Applications/Life Sciences
Source0: newbler_CLI_2.6.x86_64.tgz
Packager: TACC - vaughn@tacc.utexas.edu
BuildRoot: /var/tmp/%{name}_%{version}-buildroot
%include rpm-dir.inc
%include ../system-defines.inc
# Compiler Family Definitions
# %include compiler-defines.inc
# MPI Family Definitions
# %include mpi-defines.inc
# Other defs
%define PNAME %{name}
%define INSTALL_DIR %{APPS}/%{PNAME}/%{version}
%define MODULE_DIR %{APPS}/%{MODULES}/%{PNAME}
%define MODULE_VAR TACC_NEWBLER
%description
Newbler is the assembler designed to work with 454 sequencing reads, although it can use reads from other sources to some extent.
%prep
rm -rf $RPM_BUILD_ROOT
%setup -n newbler_CLI_2.6.x86_64
%build
%install
%include ../system-load.inc
mkdir -p $RPM_BUILD_ROOT/%{INSTALL_DIR}
module purge
module load TACC
echo "Newbler is distributed as a compiled binary. No compilation necessary."
cp -R ./* $RPM_BUILD_ROOT/%{INSTALL_DIR}
#-----------------
# Modules Section
#-----------------
rm -rf $RPM_BUILD_ROOT%{MODULE_DIR}
mkdir -p $RPM_BUILD_ROOT%{MODULE_DIR}
cat > $RPM_BUILD_ROOT%{MODULE_DIR}/%{version}.lua << 'EOF'
help(
[[
The %{PNAME} module file defines the following environment variables:
%{MODULE_VAR}_DIR, %{MODULE_VAR}_BIN and %{MODULE_VAR}_CONFIG for the location of the %{PNAME}
distribution.
Version %{version}
]]
)
whatis("Name: Newbler")
whatis("Version: %{version}")
whatis("Category: computational biology, genomics")
whatis("Keywords: Biology, Genomics, Sequencing, Assembly")
whatis("URL: http://www.my454.com/")
whatis("Description: Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company.")
prepend_path("PATH", "%{INSTALL_DIR}/bin")
setenv ( "%{MODULE_VAR}_DIR", "%{INSTALL_DIR}/")
setenv ( "%{MODULE_VAR}_BIN", "%{INSTALL_DIR}/bin")
setenv ( "%{MODULE_VAR}_CONFIG", "%{INSTALL_DIR}/config")
EOF
#--------------
# Version file.
#--------------
cat > $RPM_BUILD_ROOT%{MODULE_DIR}/.version.%{version} << 'EOF'
#%Module3.1.1#################################################
##
## version file for %{PNAME}-%{version}
##
set ModulesVersion "%{version}"
EOF
%files
%defattr(755,root,root,-)
%{INSTALL_DIR}
%{MODULE_DIR}
%clean
rm -rf $RPM_BUILD_ROOT
(53) Ray
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
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Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
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Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
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Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
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If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see .
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read .
(54) MIRA
1.6.2. License
1.6.2.1. MIRA
MIRA has been put under the GPL version 2.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
You may also visit http://www.opensource.org/licenses/gpl-2.0.php at the Open Source Initiative for a copy of this licence.
1.6.2.2. Documentation
The documentation pertaining to MIRA is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.
1.6.3. Copyright
© 1997-2000 Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecular Biophysics and Bastien Chevreux (for MIRA) and Thomas Pfisterer (for EdIt)
© 2001-2013 Bastien Chevreux.
All rights reserved.
(55) EMBOSS Suite
EMBOSS License
The AJAX and NUCLEUS libraries are released under the GNU Library General Public Licence.
EMBOSS applications are released under the GNU General Public Licence.
Parsing of ACD files does not constitute a "derived work" and developers are encouraged to do this, for example to write their own GUIs.
For developers who have their own licensing conditions already in effect, there will be an additional way to contribute. The EMBASSY collection can include packages that use the EMBOSS core libraries and interfaces but under their own licensing conditions. They will be bound by the Library GPL of the AJAX and NUCLEUS libraries, but not necessarily by the full GPL.
For more information on how to develop your own EMBOSS applications, contact emboss-bug@emboss.open-bio.org
(56) SMRT pipeline
Notices, Terms, Conditions and Use Restrictions Pertaining to Use of Pacific Biosciences Products and/or Third Party Products
Terms and Conditions of Sale
Software End User License Agreement
Third Party Software Notices, Terms, Conditions and/or Use Restrictions
TERMS AND CONDITIONS OF SALE
Attention Purchasing Department: to facilitate prompt processing of your purchase order by PacBio, please be sure that your order form does not contain or incorporate by reference any terms or conditions different from, or in addition to, the Quotation(s) (if any) and these Terms. If your order form includes, or makes reference to, any different or additional terms or conditions, please include the following statement prominently on your order form:
"Any conflict between the parties' respective sales/purchase terms and conditions shall be resolved by giving them priority in the following order: (1) the sales quotation(s) (if any) issued by Pacific Biosciences; (2) the following terms of this order: name and identity of the product(s) and/or services purchased, quantity, bill to and ship to address, and, if accurate, price; (3) Pacific Biosciences' Terms and Conditions of Sale; and (4) any other terms and conditions contained in, or incorporated by reference into, this order."
Attention Contracting Officer (U.S. Government agencies only): If PacBio is responding to a solicitation or is awarded a contract, such response or contract is subject to the following terms and conditions, which constitute "Addenda to this solicitation or contract, including any license agreements for computer software" for purposes of FAR 52.212-4 (Contract Terms and Conditions—Commercial Items), and, accordingly, are incorporated by reference into item # 4 of paragraph (s) (Order of Precedence) thereof.
DEFINITIONS AND RELATED MATTERS
1.1 "Product" means each item, including any PacBio Instrument, Licensed Software and/or PacBio Consumable, listed in the applicable written sales quotation issued by PacBio ("Quotation") or, in the event a Quotation is not issued, listed in PacBio's then-current price list applicable to Buyer's jurisdiction, and identified in Buyer's purchase order.
1.2 "PacBio Instrument" means a PacBio-branded instrument (including any PacBio® RS sequencing instrument).
1.3 "PacBio Consumables" means PacBio SMRT® Cells and/or associated PacBio-branded reagent kits, and labware intended by PacBio for use with PacBio Instruments.
1.4 "Licensed Software" means the (i) PacBio Instrument operating system software and firmware, including PacBio Instrument control, data collection and the PacBio Instrument's touch screen user interface ("O/S Software"), (ii) PacBio primary analysis software, including signal processing, base calling and quality assessment functions ("Primary Analysis Software"), and (iii) the software included with the RS Insight service feature (see Section 7.3 below), in each case provided by PacBio to Buyer pre-installed on, and/or on DVD or other media delivered with, a PacBio Instrument, and/or made available by PacBio for download, in object code or executable form only.
1.5 "Documentation" means the user documentation accompanying, or provided by PacBio regarding or for use in connection with, a Product or related service.
2. TERMS, CONDITIONS AND ORDERS
2.1 Terms and Conditions. These terms and conditions of sale ("Terms") along with any Quotation(s) issued by Pacific Biosciences of California, Inc. or its subsidiary identified on the Quotation(s) ("PacBio") and any applicable licenses, notices, terms, conditions or use restrictions listed in Section 3.1, together with any addenda to any of the foregoing provided by PacBio, any other terms and conditions expressly agreed to in writing by an authorized PacBio representative expressly referencing these Terms, and Buyer's statement on its purchase order (if accepted by PacBio) of the name and identity of the Product(s) and/or related services purchased, quantity, bill to and ship to address, and, if accurate, price (and only such information on Buyer's purchase order), shall govern the sale and license of any Product(s) (except for Licensed Software, which is only licensed, never sold) by PacBio to the purchaser ("Buyer"), and shall constitute the complete, exclusive and entire agreement ("Agreement") between PacBio and Buyer with respect to purchase and/or license of the Product(s) and any related services from PacBio. PacBio's offer to sell products and provide any related services is expressly limited to the terms of this Agreement. In the event of any conflict between the terms of the Quotation and these Terms, the terms of the Quotation shall take precedence. Buyer's submission of a purchase order or other instrument for or regarding the purchase of Product(s) or related services from PacBio, whether or not in response to a PacBio quotation, shall be deemed an acceptance of and agreement to the terms of this Agreement to the exclusion of any other terms and conditions contained in and/or referenced by such purchase order or other instrument (except the name and identity of the Product(s) purchased, quantity, bill to and ship to address, and, if accurate, price), which are hereby deemed to be material alterations, and notice of objection to which is hereby given, notwithstanding anything to the contrary contained within such purchase order or other instrument or elsewhere. Any acceptance by PacBio of any offer of Buyer as provided in any Buyer purchase order or other instrument is expressly conditioned upon Buyer's assent to and acceptance of the terms of this Agreement to the exclusion of any terms in Buyer's purchase order or other instrument that are in any way inconsistent with the terms of this Agreement.
2.2 Acceptance of Orders. No purchase order shall be binding upon PacBio unless and until accepted by PacBio in writing, and PacBio shall have no liability or obligation to Buyer with respect to orders that are not accepted. No partial shipment of an order shall constitute the acceptance of the entire order, absent the written acceptance of such entire order. For PacBio Instrument orders, PacBio may require Buyer to identify in its purchase order the individual responsible for ensuring that Buyer provides a prepared and available installation site in accordance with PacBio's site preparation specifications. Any provision in Buyer's Terms (if applicable) permitting Buyer at its convenience to unilaterally change or cancel its purchase order (in whole or part) once accepted by PacBio shall be void and of no effect.
2.3 Contract Documents & Order of Precedence. Notwithstanding Section 2.1 above, if a purchase order from Buyer that is accepted by PacBio contains or incorporates by reference any different or additional terms and conditions, and to the extent such different or additional terms and conditions are ultimately deemed part of the contract between Buyer and PacBio regarding such purchase order (e.g., by express written agreement of the parties, or by application of legal doctrine), then such contract shall consist of the following documents (notwithstanding any provision in such documents to the contrary): (1) the Quotation(s) (if any) issued by PacBio; (2) the following terms of Buyer's order: name and identity of the Product(s) and/or related services purchased, quantity, bill to and ship to address, and, if accurate, price; (3) these Terms; and (4) any other terms and conditions contained in, or incorporated by reference into, Buyer's order. Any conflict among these documents shall be resolved by giving them priority in the order listed above. Items (2) and (4) are collectively referred to herein as "Buyer's Terms."
3. LICENSE AND USE RESTRICTIONS
3.1 Limited License. Subject to these Terms, and to all applicable end user license agreement(s), notices, terms, conditions and/or use restrictions (i) printed on any Product packaging, label or insert, (ii) appearing in or included with the Licensed Software or any Documentation, or (iii) listed on PacBio's website at http://www.pacificbiosciences.com/licenses.html, PacBio grants to Buyer a non-exclusive, non-transferable, non-sublicensable license to use the Product(s) sold and/or licensed to Buyer by PacBio or its authorized distributor only in accordance with the applicable, then-current Documentation. Buyer is also authorized to use, in connection with the Product(s) sold and/or licensed to Buyer by PacBio or its authorized distributor, standard laboratory reagents, tools and equipment ancillary to the use of such Product(s), as provided in the applicable, then-current Documentation, and to conduct library preparation and sample labeling protocols utilized by Buyer, in connection with Buyer's use of such Product(s), provided that the foregoing shall not be construed as granting, by implication, estoppel or otherwise, any license or authorization to Buyer with regard to such reagents, tools, equipment or protocols per se. No other license or authorization is granted, by implication, estoppel, or otherwise.
3.2 Certain Use Restrictions. Each Product is subject to the following terms, conditions, and restrictions, to which Buyer hereby agrees: (a) except as otherwise provided in the applicable, then-current Documentation, each Product may be used only with other Products; and (b) PacBio Consumables are licensed for SINGLE USE ONLY and MAY NOT BE REUSED. Buyer is not licensed or authorized to, and agrees not to: (i) use any PacBio Consumable more than once, (ii) transfer (including but not limited to resell, donate, or loan) any PacBio Consumable to any third party; or (iii) adapt, modify or reverse engineer any Product. Documentation is proprietary to PacBio and may only be used in connection with the associated Product(s). For clarity, and subject to these Terms (including, without limitation, Section 11), Buyer shall not be deemed to have transferred any PacBio Consumable, or transferred or granted a sub-license under the license in Section 3.1, in violation of these Terms to the limited extent that Buyer permits access to and proper use of the Products (as otherwise permitted herein) at Buyer's premises by a visiting scientist pursuant to Buyer's bona fide research collaboration with such scientist's employer. All license restrictions specified in this Section 3 and elsewhere in these Terms shall apply to the maximum extent permissible under applicable law. If Buyer believes that it has additional rights or the right to act contrary to the express license restrictions specified in these Terms under mandatory laws (including, without limitation, national laws implementing Directive 91/250/EEC and similar laws), Buyer agrees that it shall provide PacBio with at least thirty (30) days prior written notice and any reasonably requested information before exercising such rights, to allow PacBio to offer alternatives at PacBio's sole discretion.
3.3 Regulatory Compliance. Buyer acknowledges that the Products do not have United States Food and Drug Administration ("FDA") or equivalent non-U.S. regulatory agency approval ("Approval"). Accordingly, Buyer acknowledges that the Products are labeled and intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES. The Products should be used by qualified professionals in strict accordance with applicable instructions, warnings and other information in user manuals and other Documentation. Unless otherwise expressly stated by PacBio in writing, no claim or representation is made or intended by PacBio (i) as to any diagnostic or other clinical use of a Product; (ii) that any Product has any Approval for use in any diagnostic or other clinical procedure, or for any other use requiring compliance with any law, regulation or governmental policy concerning medical devices, laboratory tests or the like (collectively, "Regulatory Laws"); (iii) that any Product will satisfy the requirements of the FDA or any other regulatory agency; or (iv) that any Product or its performance is suitable or has been validated for clinical or diagnostic use, for safety and effectiveness, for any specific use or application, or for importation into Buyer's jurisdiction. Buyer agrees that if it elects to use a Product for a purpose that would subject Buyer, its customers or any Product to the application of Regulatory Laws or any other law, regulation or governmental policy, Buyer shall be solely responsible for obtaining any required Approvals and otherwise ensuring that the importation of the Products into Buyer's jurisdiction and Buyer's use of Products complies with all such laws, regulations and policies. The burden of proof for safe use and handling of Products sold to Buyer is entirely the responsibility of Buyer.
4. PRICES, TAXES AND PAYMENT
4.1 Prices. The price for any Product or related service shall be the applicable price stated in PacBio's written Quotation to Buyer, or, if no Quotation is issued, in PacBio's then-current price list applicable to Buyer's jurisdiction, provided that PacBio's Quotations are only valid for thirty (30) days from the quotation date unless otherwise stated in the Quotation.
4.2 Taxes; Shipping Charges. Unless otherwise expressly indicated in the Quotation, Buyer's purchase price does not include any U.S. or non-U.S. federal, state, local, sales, VAT, GST or other taxes, duties, or other governmental assessments ("Taxes") that may be applicable to the Products, any related services or the sale thereof, nor does the price include freight and insurance; Buyer will be responsible for any such charges specified on PacBio's invoice(s). Unless otherwise expressly indicated in the Quotation, Products will be shipped "Freight Prepaid and Added" (i.e., charged back to Buyer on PacBio's invoice) and any provision to the contrary in Buyer's Terms (if applicable) shall be void and of no effect. All Taxes shall be paid or reimbursed by Buyer (other than taxes on PacBio's net income), or in lieu thereof, Buyer shall provide PacBio with a tax exemption certificate acceptable to the applicable taxing authorities. Taxes and other charges payable by Buyer may be billed as separate items on PacBio's invoice. Buyer shall be solely responsible for any non-United States withholding taxes (e.g., if Buyer is located or incorporated outside the United States) and if withholding taxes apply, Buyer shall gross up the amount payable to ensure post-withholding remittance to PacBio at the amounts quoted and invoiced by PacBio.
4.3 Payment. Unless otherwise specifically indicated in the Quotation, PacBio shall invoice Buyer for a Product and any related services ordered by Buyer upon shipment of the Product, or after acceptance or deemed acceptance by Buyer pursuant to Section 5.3 in the case of a PacBio Instrument, or upon PacBio's acceptance of Buyer's purchase order in the case of a Service Contract, and such invoice shall cover Buyer's purchase price for the Product and/or related services and any freight, insurance, Taxes or other applicable costs initially paid or payable by PacBio to be ultimately borne by Buyer, and Buyer shall pay all such amounts. Unless otherwise expressly indicated in the Quotation or, in the event a Quotation is not issued, in PacBio's then-current price list applicable to Buyer's jurisdiction, all invoices shall be issued and payable in U.S. Dollars, and are due and payable thirty (30) days from date of invoice, subject to credit approval. Each delivery shall be considered a separate and independent transaction and payment therefor made accordingly. Amounts outstanding sixty (60) or more days from the date of invoice shall be subject to a service charge of one percent (1.0%) per month (or the maximum allowed by applicable law, if less). (Notwithstanding the foregoing, if Buyer is an agency of the U.S. Government, payment will be made in accordance with the Prompt Payment Act, 31 U.S.C. 39 et seq.) Buyer shall pay all of PacBio's costs and expenses (including reasonable attorneys' fees) to enforce and preserve PacBio's rights under this section. If Buyer fails to make any payment when due or if PacBio deems Buyer to be or to have become un-creditworthy, then, without prejudice to PacBio's rights, PacBio may, at its option, cancel and/or suspend future deliveries, and/or require prepayment, letter of credit, or other payment method(s) in PacBio's discretion. The amount of credit may be changed or credit withdrawn by PacBio at any time. PacBio may elect to retain title to Products and any resale purchase price claims, until PacBio receives payment in full, and where title retention is not fully valid or enforceable, PacBio may elect to retain a security interest in Products sold to Buyer to secure Buyer's payment obligations to PacBio, and Buyer will execute any documents necessary to create and perfect this interest.
5. DELIVERY AND ACCEPTANCE OF PRODUCTS
5.1 Delivery. Unless otherwise expressly indicated in the Quotation, all deliveries to destinations within the United States are F.O.B. shipping point, and all deliveries to destinations outside the U.S. are FCA Origin (ICC Incoterms 2010) PacBio's shipping dock. Without limiting the generality of PacBio's rejection of Buyer's conflicting terms, any provision to the contrary in Buyer's Terms (if applicable) shall be void and of no effect. PacBio's title (except for Licensed Software, which is only licensed, never sold), and all risk of loss, passes to Buyer, and PacBio's liability as to delivery ceases, upon delivery of the Products at the F.O.B./FCA point. Unless specific shipping instructions have been agreed between PacBio and Buyer, PacBio will ship in accordance with its standard practices. Any provision in Buyer's Terms (if applicable) indicating that time is "of the essence" (or other terms of similar import) for delivery or other performance by PacBio shall be void and of no effect. Delivery of Products shall be in accordance with PacBio's then applicable manufacturing schedule and based upon a priority of 'first order accepted, first order shipped' basis. Notwithstanding the foregoing, PacBio, in its sole discretion, may reprioritize scheduling of any delivery or deliveries of any orders accepted by PacBio. PacBio may also, in its sole discretion, postpone delivery of a PacBio Instrument due to Buyer's failure to provide a prepared and available installation site in accordance with PacBio's site preparation specifications or other factors within Buyer' reasonable control. For multiple unit and/or multiple Product orders PacBio may make delivery in installments, and each installment shall be deemed to be a separate sale. PacBio may issue a separate invoice for each installment, which invoice shall be paid without regard to prior or subsequent installments. Buyer must notify PacBio of any damaged or missing Products within fifteen (15) days after receipt. Products rejected by Buyer will be held by Buyer and may be returned only upon PacBio's written authorization. PacBio shall be entitled to repair or replace damaged, missing, and/or rejected Products. These are Buyer's sole and exclusive remedies for rejected Products.
5.2 PacBio Instrument Inspection and Installation. Without limiting the preceding section, Buyer shall promptly uncrate and visually inspect any PacBio Instrument upon receipt and notify PacBio in writing of receipt of the PacBio Instrument and any damage or missing parts that Buyer notes. Buyer shall ensure that a PacBio representative is present and is permitted to supervise the uncrating and inspection of the PacBio Instrument. If Buyer fails to comply with this section, Buyer shall be deemed to have waived its rights to claim incorrect or incomplete delivery or packaging and any related warranty rights. If PacBio has agreed to install the PacBio Instrument, it is Buyer's responsibility, at Buyer's cost, to have the installation site prepared and available for installation in accordance with PacBio's site preparation specifications and free of hazardous or unsafe conditions and, unless otherwise agreed, to move the PacBio Instrument from Buyer's delivery dock or receiving location to the place of installation. Buyer shall have appropriate Buyer personnel present at any such installation. Buyer shall not assign PacBio personnel to work in biosafety level 3 or level 4 laboratories without prior written notice to PacBio and PacBio's prior written consent.
5.3 PacBio Instrument Acceptance. Acceptance or rejection of any PacBio Instrument shall be based exclusively on PacBio' published specifications and the results of PacBio's standard site acceptance testing procedure ("SAT") in effect at the time of delivery. Buyer shall provide PacBio with on-site and remote access to the PacBio Instrument (and any related hardware or software) for such purposes. At Buyer's request, a Buyer representative may attend the SAT. Within ten (10) days of successful SAT completion, as evidenced by the written report to be provided by PacBio to Buyer, Buyer shall sign a written acceptance statement, using the form to be provided by PacBio, and such acceptance will represent Buyer's acceptance of the Instrument based on the Instrument's performance as delivered, without consideration of potential future performance enhancements. If the PacBio Instrument fails the SAT, then PacBio shall use commercially reasonable efforts to remedy any non-conformance and repeat the SAT process. In the absence of an express acceptance, Buyer shall be deemed to have irrevocably accepted any PacBio Instrument upon the earlier of (i) payment, without reservation, of any amounts with respect to the PacBio Instrument; (ii) ten (10) days after Buyer's receipt of PacBio's report evidencing successful completion of the SAT; (iii) Buyer's use of the PacBio Instrument (outside of the SAT); or (iv) within thirty (30) days after delivery of the PacBio Instrument if PacBio is unable to perform installation or the SAT due to Buyer's failure to provide a prepared and available installation site in accordance with PacBio's site preparation specifications or other factors within Buyer' reasonable control.
6. LIMITED WARRANTIES
6.1 Limited Warranty and Remedy for PacBio Instruments and O/S Software. PacBio warrants, only to Buyer, that as of the date the PacBio Instrument is accepted or deemed accepted by Buyer pursuant to Section 5.3 (the "Warranty Effective Date"), each PacBio Instrument (including its O/S Software as provided by PacBio, provided that Buyer maintains a software release level within one major release of the most current O/S Software release made available by PacBio to Buyer at no additional charge, but excluding any other software and also excluding any external uninterruptable power supply (UPS)) purchased by Buyer from PacBio hereunder, as delivered and under normal use and service, will conform in all material respects to PacBio's published specifications in effect at the time of delivery and will be free from defects in material and workmanship under normal use and service, unless the applicable Quotation or Documentation states that a different warranty or no warranty is provided by PacBio. Buyer's exclusive remedy, and PacBio's sole liability and obligation, under this warranty is limited to replacing, repairing or giving credit for, at PacBio's option, any PacBio Instrument for which written notice of the nonconformity is provided to PacBio within a period of twelve months (or such other period as stated in the applicable Quotation or Documentation) following the Warranty Effective Date (the "Warranty Period"). PacBio Instrument repairs will be effected on-site at Buyer's facility, except to the extent that PacBio approves removal and return of particular components to PacBio for repair or replacement, and except for remote diagnostics, maintenance and repair (see description of PacBio's RS Insight service feature in Section 7.3 below) or delivery of updated or corrected O/S Software for replacement purposes. Any such approved Buyer returns shall be shipped to PacBio's designated facility in accordance with PacBio's return procedures, at PacBio's expense. O/S Software warranty nonconformities are limited to errors that cause the covered PacBio Instrument hardware to fail to conform to this warranty, and will be addressed by PacBio commensurate with the severity of the nonconformity; PacBio does not warrant that any particular O/S Software warranty nonconformity will be corrected, or a workaround provided, within any particular time frame, provided that any O/S Software warranty nonconformities preventing the covered PacBio Instrument hardware from conforming to this warranty shall be remedied by PacBio within a commercially reasonable timeframe (taking into account the nature of the Products). Without limiting the foregoing warranty, repairs and replacements may be effected prior to acceptance or during the Warranty Period with reconditioned or refurbished Products, parts or subassemblies. This limited warranty is subject to certain exceptions listed below.
6.2 Limited Warranty and Remedy for Primary Analysis Software. PacBio warrants, only to Buyer, that on the Warranty Effective Date of a particular PacBio Instrument purchased by Buyer from PacBio hereunder, the Primary Analysis Software, as provided by PacBio, when properly installed and used in connection with that PacBio Instrument, as set forth in the applicable Documentation, will function substantially in accordance with the functions and features described in such Documentation, provided that Buyer maintains a software release level within one major release of the most current release of the Primary Analysis Software made available by PacBio to Buyer at no additional charge. Buyer's exclusive remedy, and PacBio's sole liability and obligation, under this warranty are limited to using reasonable efforts, commensurate with the severity of the nonconformity, to correct, or, at PacBio's option, giving credit for, any substantial nonconformity of the Primary Analysis Software for which written notice is provided to PacBio within the Warranty Period. PacBio does not warrant that use of Primary Analysis Software will be uninterrupted or error free, or that any particular Primary Analysis Software warranty nonconformity will be corrected, or a workaround provided, within any particular time frame. This limited warranty is subject to certain exceptions listed below.
6.3 Limited Warranty and Remedy for Third Party Computing Systems. PacBio warrants, only to Buyer, that as of the date of delivery, each third party computing system (including its operating system software as provided by PacBio, provided that Buyer maintains a software release level within one major release of the most current operating system software release made available by PacBio or the original equipment manufacturer or licensor at no additional charge to Buyer, but excluding any other software and also excluding any external uninterruptable power supply (UPS)) purchased by Buyer from PacBio hereunder, as delivered and under normal use and service, will conform in all material respects to PacBio's published specifications in effect at the time of delivery and will be free from defects in material and workmanship, unless the applicable Quotation or Documentation states that a different warranty or no warranty is provided by PacBio. Buyer's exclusive remedy, and PacBio's sole liability and obligation, under this warranty is limited to replacing, repairing or giving credit for, at PacBio's option, any third party computing system for which written notice of the nonconformity is provided to PacBio within a period of twelve months (or such other period as stated in the applicable Quotation or Documentation) following the date of delivery. Third party computing system repairs will be effected on-site at Buyer's facility, except to the extent that PacBio approves removal and return of particular components to PacBio for repair or replacement, and except for remote diagnostics, maintenance and repair or delivery of updated or corrected operating system software. Any such approved Buyer returns shall be shipped to PacBio's designated facility in accordance with PacBio's return procedures, at PacBio's expense. Operating system software warranty nonconformities are limited to errors that cause the covered third party computing hardware to fail to conform to this warranty, and will be addressed by PacBio or its designee commensurate with the severity of the nonconformity; PacBio does not warrant that any particular operating system software warranty nonconformity will be corrected, or a workaround provided, within any particular time frame, provided that any operating system software warranty nonconformities preventing the covered third party computing hardware from conforming to this warranty shall be remedied by PacBio or its designee within a commercially reasonable timeframe (taking into account the nature of the Products). Without limiting the foregoing warranty, repairs and replacements may be effected with reconditioned or refurbished Products, parts or subassemblies. This limited warranty is subject to certain exceptions listed below.
6.4 Limited Warranty and Remedy for Consumables. PacBio warrants, only to Buyer, that each PacBio Consumable purchased by Buyer from PacBio hereunder will be free from defects in material and workmanship upon delivery to Buyer. All PacBio Consumable warranty remedies are subject to the condition that warranty claims must be received by PacBio in writing no later than thirty (30) days after the earlier of any shelf life date, expiration date, "use by" date, "guarantee date" or other end of recommended use date, or the date the number of uses stated on the PacBio Consumable's label or in the accompanying Documentation is reached. Buyer's exclusive remedy, and PacBio's sole liability and obligation, under this warranty are replacing, or, at PacBio's option, giving credit for, any PacBio Consumable not meeting the above warranty for which written notice is provided to PacBio within the applicable period. If the defect(s) in material and workmanship diminished but did not prevent performance of the PacBio Consumable, any amount refunded may be apportioned according to PacBio's reasonable allocation of the value of the diminished performance. The decision of whether to replace the PacBio Consumable or give credit will be made by PacBio in its sole discretion. Notwithstanding the foregoing, custom PacBio Consumables made to specifications of Buyer are sold "AS IS", without any warranty whatsoever, express or implied, except to the extent set forth in any separate express written limited warranty included in the Documentation provided with the PacBio Consumable or in the Quotation. Except as set forth above, expiration dates, shelf life, "use by," guaranty or other end of recommended use dates are included for informational purposes only and shall not be deemed as a period of warranty. This limited warranty is subject to certain exceptions listed below.
6.5 Limited Warranty and Remedy for Service Parts. PacBio warrants, only to Buyer, that spare, replacement or upgrade parts (collectively, "Service Parts"), including PacBio Instrument hardware upgrades, that are purchased by Buyer from PacBio hereunder and installed by a PacBio service engineer subsequent to PacBio Instrument installation will be free of defects in materials and workmanship on the date of delivery, provided that PacBio receives Buyer's written warranty claim during a period of the earlier of ninety (90) days from the date of installation or one hundred twenty (120) days from the date of delivery. Buyer's exclusive remedy, and PacBio's sole liability and obligation, under this warranty are replacing, at PacBio's option, giving credit for, any Service Parts not meeting the above warranty for which written notice is provided to PacBio within the applicable period. Service Parts that are not installed by a PacBio service engineer are sold "AS IS," without any warranty, statutory, express or implied. The installation of a PacBio Instrument hardware upgrade does not extend or restart any PacBio Instrument warranty, but the parts comprising the PacBio Instrument upgrade are covered by the foregoing Service Parts limited warranty to the extent applicable. This limited warranty is subject to certain exceptions listed below.
6.6 Exceptions. These warranties shall not apply to, and shall be void for, any Product that (i) was subject to improper or abnormal use, abuse, neglect, negligence, accident, including without limitation failure to properly perform routine maintenance and maintain the Product site in accordance with PacBio's site requirements or the use of the Product with any non-PacBio product (except as may be specifically recommended, with respect to standard laboratory reagents, tools and equipment ancillary to use of the Product, in the then-current Documentation for that Product); (ii) has been repaired, altered, disassembled, reassembled or removed from Buyer's facility by persons other than PacBio or its designee, other than repair or replacement of a third-party good by an authorized service provider; or (iii) has failed due to externally caused short circuits, incorrect voltages, failure or fluctuation of electrical power, lightning, static or other improper external inputs, or due to Force Majeure. For clarity, and without limitation, use of a PacBio Instrument with consumables other than the PacBio Consumables specified for use with that PacBio Instrument, will void the warranty for that PacBio Instrument. Any Buyer attempt to repair or otherwise alter any Product, except as may be specifically pre-authorized by PacBio in writing in each case, and except for cleaning and replenishment of disposable components (tips), sample drawers and reagent reservoirs, and emptying of waste receptacles, per the applicable Documentation, shall void the warranty for that Product. Without limiting the foregoing, with regard to Licensed Software, these warranties shall not apply to any failure to conform that is caused by the use or operation of the Licensed Software in an environment other than that intended or recommended by PacBio, or modifications to the Licensed Software not made or authorized by PacBio. PacBio makes no standalone warranty with regard to Licensed Software. These warranties are not transferable or assignable, including without limitation, in any re-sale of a PacBio Instrument or third party computing system, and any such attempt to transfer or assign these warranties shall be void for any unit to which they apply. Notwithstanding the foregoing, these warranties may be assigned for any PacBio Instrument that is acquired as a business asset in conjunction with a merger or acquisition of Buyer or of all or substantially all of Buyer's business assets of which the PacBio Instrument is a part. PacBio neither assumes, nor authorizes any other person to assume for it, any other obligations or liabilities in connection with the sale of Products. Repair or replacement of a Product shall not extend the original warranty period for that Product. PacBio's warranties do not cover de-installation, re-installation, or transportation of products.
7. PACBIO INSTRUMENT SUPPORT; LIMITED SERVICE WARRANTY.
7.1 Service and Maintenance. During the Warranty Period for a PacBio RS sequencing instrument purchased by Buyer from PacBio hereunder, PacBio will provide its standard level of service and maintenance for such PacBio Instrument (equivalent to PacBio's "Standard" level Service Contract) at no additional charge to Buyer. After the Warranty Period, PacBio may offer to provide extended service and maintenance for such PacBio Instrument pursuant to separate written service contracts that may be purchased by Buyer from PacBio. Extended service and maintenance for any third party computing system must be obtained by Buyer directly from the original manufacturer.
7.2 Service Contracts. If Buyer has purchased a separate written service contract from PacBio for a PacBio Instrument (a "Service Contract"), the Quotation and the applicable, then-current Documentation for such Service Contract describe its level and features, including minimum response times and the number of preventative maintenance visits per year. During the Service Contract term, PacBio or its designee will provide the services described in the Service Contract (the "Covered Services"). Maintenance, repairs and replacements may be effected under the Service Contract with reconditioned or refurbished Products, parts or subassemblies. Any updates or upgrades to the Licensed Software, when delivered, shall become part of the Licensed Software and shall be subject to the same end user license agreement(s), notices, terms, conditions and use restrictions unless otherwise expressly stated in writing by PacBio. Covered Services exclude hardware upgrades for feature enhancements. Service Contracts may not be transferred or assigned without PacBio's prior written consent.
7.3 Remote Support. Certain Service Contract levels and/or features require the use of PacBio's RS Insight service feature, which includes remote communication software that allows a PacBio authorized agent to remotely communicate with the PacBio RS sequencing instrument purchased by Buyer through user-controlled, customizable permission settings. The RS Insight service feature is used by PacBio for diagnostics, maintenance and repair of the PacBio RS instrument hardware and software components, and may allow for faster response times if Buyer purchases a Service Contract that includes the RS Insight service feature and abides by the configuration requirements specified by PacBio. If Buyer purchases a Service Contract with the RS Insight service feature and elects to also utilize the optional policy server software, Buyer agrees to configure the policy server software to enable PacBio to provide the Covered Services as specified in the Service Contract. Buyer acknowledges that any faster response times will be honored by PacBio only if proper internet connectivity has been established by Buyer and the software included with the RS Insight service feature (including the policy server software, if applicable) is configured to, and Buyer actually does, permit PacBio throughout the term of the Service Contract (with at least the frequency, if any, specified by PacBio for each such activity) to (i) establish SSH sessions for the transfer of instrument performance data files to PacBio, (ii) retrieve instrument environmental data values, (iii) utilize event and alarm functionality, and (iv) effect remote software updates and software file transfers.
7.4 Service Limitations. Buyer agrees to follow the operation procedures published by PacBio, including procedures for routine maintenance. PacBio shall have no obligation to provide any service or parts required as a result of (i) failure of Buyer to maintain a software release level within one major release of the most current O/S Software release made available by PacBio to Buyer at no additional charge, (ii) improper or abnormal use, abuse, neglect, negligence, accident, including without limitation failure to properly perform routine maintenance and maintain the PacBio Instrument site in accordance with PacBio's site requirements or the use of the PacBio Instrument with any non-PacBio product (except as may be specifically recommended, with respect to standard laboratory reagents, tools and equipment ancillary to use of the Product, in the then-current Documentation for that Product); (iii) repairs, alterations, disassembly, reassembly or removal from Buyer's facility by persons other than PacBio or its designee, other than repair or replacement of a third-party good by an authorized service provider; or (iv) externally caused short circuits, incorrect voltages, failure or fluctuation of electrical power, lightning, static or other improper external inputs, or Force Majeure. Buyer shall reimburse PacBio at PacBio's then-current service call fees, including all labor, parts and travel charges, for all work of PacBio or its designee incurred in investigating or remedying any damage or malfunction that PacBio reasonably determines to not be part of the Covered Services.
7.5 Non-Covered Equipment. Any and all instruments, software and other products, and any parts or subassemblies of the foregoing, that are not provided by PacBio or its designee, as well as any external uninterruptible power supply (UPS), shall be deemed "Non-Covered Equipment." PacBio shall have no obligation to provide Covered Services for Non-Covered Equipment; moreover, and notwithstanding anything herein to the contrary, PacBio shall have no obligation to provide Covered Services in connection with any PacBio Instrument, part or subassembly: (i) that has been substantially altered (other than by PacBio or its designee), including any alteration or removal of any serial numbers or other identifying markings; (ii) that does not incorporate all of PacBio's engineering improvements and other fixes that PacBio requests Buyer to implement; (iii) that incorporates Non-Covered Equipment or has Non-Covered Equipment attached; (iv) that has been operated in conditions outside of PacBio's environmental or electrical site specifications, as defined in the applicable, then-current Documentation; (v) that has been operated in hazardous environments or used to analyze hazardous materials that may cause residual contamination; or (vi) that has been repaired or maintained by anyone other than PacBio or its designee, except such routine maintenance as set forth in the applicable, then-current Documentation. PacBio Instruments that are no longer offered for sale by PacBio ("Obsoleted Items") will be maintained and repaired on a reasonable efforts basis by PacBio while covered by a Service Contract. If PacBio determines in its discretion that support, service or maintenance of such Obsoleted Items is no longer reasonable, PacBio shall notify Buyer of such determination and such Obsoleted Item shall be deemed Non-Covered Equipment.
7.6 Billable Services. All services performed by PacBio or its designee on Buyer's Non-Covered Equipment or which are not Covered Services shall be billable to Buyer at PacBio's then-current service call fees, including all labor, parts and travel charges.
7.7 Access and Service Safety. Buyer will provide PacBio and its designees reasonable and safe access to all PacBio Instruments for the provision of any services and for any audit of compliance with PacBio's installation and operational guidelines. If environmental or operational contamination creates a hazard for PacBio personnel, PacBio may instead elect to supervise Buyer's performance of service procedures. Buyer is responsible for proper disposal of all contaminated material and of contaminated parts and subassemblies that, in PacBio's discretion, cannot be safely returned to PacBio. Any services that PacBio or its designee may provide in connection with the activities contemplated by this paragraph shall be deemed to not be Covered Services, and Buyer shall reimburse PacBio at PacBio's then-current service call fees, including all labor, parts and travel charges, for all such work of PacBio or its designee.
7.8 PacBio Instrument Relocation. If any PacBio Instrument is moved from its installation position, PacBio may, at its discretion, determine that such PacBio Instrument has been relocated (a "Relocation"). Relocation of PacBio Instruments may result in service charges as follows: (i) Approved Relocation. Relocation of PacBio Instruments by PacBio or its designees is permitted. PacBio Instruments may be moved with the assistance of PacBio at PacBio's service call fees, including all labor, parts and travel charges. With prior written approval of PacBio, Buyer may move specified PacBio Instruments without incurring any charges. Buyer will contact PacBio prior to moving any PacBio Instrument. (b) Unapproved Relocation. Any service contract or warranty covering a PacBio Instrument shall be rendered void and unenforceable by Relocation of such PacBio Instrument without the prior written approval of PacBio. At the discretion of PacBio, upon completion of a maintenance inspection and service at PacBio's then-current service call fees, including all labor, parts and travel charges, the subject service contract or warranty may be reinstated. (c) New Site Location. Relocation of PacBio Instruments may result in additional service charges and modification of response times, as determined by PacBio.
7.9 Ownership. All replaced parts removed from the PacBio Instrument in connection with any services provided by PacBio or its designee shall become the property of PacBio upon their replacement. All intellectual property rights arising from any modifications made or provided by PacBio or its designee, whether alone or with any contribution from Buyer or its employees, agents, contractors or collaborators, to the PacBio Instrument shall be owned exclusively by PacBio. To the extent Buyer or its employees, agents, contractors or collaborators may acquire any right or interest therein by operation of law, Buyer hereby irrevocably assigns all such rights and interests exclusively to PacBio. Buyer shall maintain and enforce agreements and policies with its employees, agents, contractors and collaborators sufficient to give effect to the provisions of this section.
7.10 Limited Service Warranty. PacBio warrants that it will render the Covered Services in a professional and workmanlike manner. As PacBio's sole responsibility and Buyer's exclusive remedy in the event of any material failure to meet such standard, PacBio shall make a commercially reasonable effort to remedy any resulting discrepancies. Any claim based on the foregoing warranty must be submitted in writing in accordance with PacBio's standard procedures within thirty (30) days after delivery or the date of performance of the pertinent services at issue.
7.11 Term and Termination. The term of a Service Contract shall commence on the date PacBio receives an authorized purchase order from Buyer, and continue as specified in the applicable Quotation describing the Service Contract or, if no such term is specified, the term shall be one year. Service Contracts shall not be automatically renewed. If Buyer wishes to obtain Covered Services for a PacBio Instrument beyond the term of the Service Contract or for additional PacBio Instruments, Buyer must submit a new order. PacBio may terminate a Service Contract immediately by giving written notice of termination to Buyer upon the occurrence of any of the following events: (i) Buyer defaults in the performance of any material requirement or obligation created by the Service Contract or any other agreement between PacBio and Buyer; (ii) Buyer fails to make any payment to PacBio within (30) days of its due date; (iii) Buyer ceases doing business; (iv) Buyer becomes the subject of any bankruptcy, insolvency, or similar proceeding, becomes insolvent, makes an assignment for the benefit of creditors, is unable to pay its debts when due, a receiver is appointed for a substantial part of Buyer's assets, or an action is taken toward the liquidation or winding up of Buyer's business; or (v) Buyer suffers a materially adverse change in its financial condition or operations. No termination of a Service Contract shall release Buyer from any obligation to pay PacBio any amount that has accrued or become payable at or prior to the date of termination. In no event (including early termination) shall PacBio be obligated to return any payments received by PacBio under a Service Contract.
8. WARRANTY DISCLAIMERS
8.1 Disclaimer; No Other Warranties. THE EXPRESS WARRANTIES AND THE REMEDIES SET FORTH IN SECTIONS 6 AND 7.10 ARE IN LIEU OF, AND PACBIO HEREBY DISCLAIMS, ALL OTHER REMEDIES AND WARRANTIES, EXPRESS, STATUTORY, IMPLIED, OR OTHERWISE, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NONINFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE, OR REGARDING RESULTS OBTAINED THROUGH THE USE OF ANY PRODUCT OR SERVICE (INCLUDING, WITHOUT LIMITATION, ANY CLAIM OF INACCURATE, INVALID OR INCOMPLETE RESULTS), IN EACH CASE HOWEVER ARISING, INCLUDING WITHOUT LIMITATION FROM A COURSE OF PERFORMANCE, DEALING OR USAGE OF TRADE, OR OTHERWISE. IN NO EVENT SHALL PACBIO BE LIABLE FOR COSTS OF SUBSTITUTE GOODS OR SERVICES OR FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR INDIRECT DAMAGES FOR BREACH OF WARRANTY. ANY PRODUCT OR SERVICE PROVIDED WITHOUT A WRITTEN WARRANTY FROM PACBIO IS PROVIDED "AS IS" WITHOUT (AND PACBIO HEREBY DISCLAIMS) ANY WARRANTY, STATUTORY, EXPRESS, IMPLIED OR OTHERWISE. Without limiting the generality of PacBio's general rejection of conflicting terms presented by Buyer, and for clarification purposes only, Buyer agrees that any different or additional warranty terms stated in Buyer's Terms (if applicable) shall be void and of no effect.
8.2 Third Party Disclaimers. Notwithstanding any provision to the contrary herein, and unless otherwise expressly indicated in the Quotation or Documentation, none of PacBio's suppliers or licensors of any Product or other item provided by PacBio, or any portion thereof (under this Agreement or otherwise) (each, a "Supplier") provides ANY WARRANTY WHATSOEVER, EXPRESS, STATUTORY, IMPLIED, OR OTHERWISE TO BUYER, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NONINFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE, AND ALL SUCH WARRANTIES ARE DISCLAIMED. EXCEPT AS OTHERWISE EXPRESSLY INDICATED IN THE QUOTATION OR DOCUMENTATION, IN NO EVENT SHALL ANY SUPPLIER BE LIABLE TO BUYER FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY, DIRECT, INDIRECT OR OTHER DAMAGES ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT AND/OR SALE OF THE PRODUCTS.
9. LIMITATION OF LIABILITY. PACBIO'S LIABILITY ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT AND/OR SALE OF THE PRODUCTS OR PROVISION OF SERVICES SHALL BE LIMITED TO THE AMOUNT PAID BY THE BUYER FOR THE PRODUCTS AND/OR SERVICES GIVING RISE TO THE LIABILITY, AND IN NO EVENT SHALL PACBIO'S AGGREGATE LIABILITY ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT AND/OR SALE OF THE PRODUCTS AND SERVICES EXCEED THE TOTAL AMOUNTS RECEIVED BY PACBIO FROM BUYER UNDER THIS AGREEMENT. IN NO EVENT SHALL PACBIO BE LIABLE FOR COSTS OF SUBSTITUTE GOODS OR SERVICES, OR FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR INDIRECT DAMAGES, HOWEVER CAUSED AND UNDER ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, TORT, WARRANTY, PURSUANT TO ANY STATUTE, OR ON ANY OTHER BASIS, ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT AND/OR SALE OF THE PRODUCTS OR SERVICES, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT PACBIO IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS OF USE, LOSS OF DATA, OR DOWNTIME, OR FOR LOSS OF REVENUE OR PROFITS. THESE LIMITATIONS SHALL APPLY NOTWITHSTANDING ANY FAILURE OF ESSENTIAL PURPOSE OF ANY LIMITED REMEDY.
10. INDEMNITY AND INSURANCE
10.1 Indemnification of Buyer. Subject to Sections 10.2 and 10.3 below, PacBio agrees to defend Buyer against any third party claim, proceeding or action ("Claim") to the extent the Claim alleges that any Product sold to Buyer hereunder, as delivered to Buyer by PacBio, directly infringes any patent, copyright, or other intellectual property right. PacBio will pay all damages awarded, and settlements approved in writing by an authorized representative of PacBio, in connection therewith, provided that (i) Buyer provides to PacBio written notice of the Claim within thirty (30) days of receipt by Buyer of such Claim, or such earlier time as required to avoid prejudice to PacBio or its ability to defend such Claim, (ii) Buyer allows PacBio to control the defense and settlement of the Claim, and (iii) Buyer provides to PacBio reasonable assistance in connection therewith, at no charge to PacBio. Buyer may employ counsel at its own expense to assist it with respect to any such Claim, provided that this shall not obligate PacBio or its counsel to consult with or advise such Buyer counsel, nor affect PacBio's control of the defense and settlement of the Claim.
10.2 Exceptions. PacBio shall have no liability or obligation pursuant to this Section 10 with respect to Claims resulting from (i) modification of the Product other than by PacBio or its authorized service provider; (ii) combination of the Product with any item or method not supplied or specifically recommended in writing by PacBio, (iii) use of the Product other than in accordance with the Documentation and this Agreement (including without limitation use for diagnostic or other non-research uses), or (iv) compliance with Buyer's instructions, specifications or design to the extent such instructions, specifications or design materially differ from comparable Products that PacBio makes generally available to its customers (collectively, (i)-(iv), "Excluded Causes").
10.3 Remedy. In the event there is a Claim, or PacBio believes a Claim is likely, alleging intellectual property infringement with respect to any Product sold to Buyer hereunder, PacBio shall be entitled, without obligation to do so, at its option and expense, to (i) modify the Product so that it is no longer infringing, (ii) obtain a license with respect to the applicable intellectual property rights, or (iii) accept the return of each such Product purchased by Buyer hereunder (except for contaminated Products that, in PacBio's discretion, cannot be safely returned to PacBio) and in Buyer's possession and control, and provide to Buyer a refund of the price paid by Buyer to PacBio therefor, subject to reasonable deductions for damage and amortized on a straight line basis over five (5) years from original delivery to Buyer. PacBio will have no liability or obligation with respect to any alleged infringement occurring after the date PacBio makes any such remedy available to Buyer.
10.4 Exclusive Obligation. Notwithstanding any other provision, the foregoing Sections 10.1-10.3 state PacBio's sole liability and obligation, and Buyer's exclusive remedy, arising out of any actual or alleged intellectual property infringement of any kind, or any actual or alleged breach of any representation or warranty (statutory, express or implied) regarding noninfringement, anywhere in the world. To the extent Buyer's Terms (if applicable) include any terms different from, or in addition to, those set forth above regarding indemnification by PacBio for intellectual property infringement claims, then such additional or different indemnity terms shall be void and of no effect. To the extent Buyer's Terms (if applicable) include any terms regarding any other type of indemnification by PacBio, then such other indemnity terms shall be void and of no effect.
10.5 Indemnification of PacBio. Buyer agrees to defend PacBio against any Claim (i) to the extent the Claim alleges infringement of any patent, copyright, or other intellectual property right as a result of any Excluded Cause, or (ii) that arises in connection with Buyer's use of Products (a) for any clinical purpose or application, (b) in violation of any applicable law or regulation, or (c) in the provision of services under any 'fee for service' agreement or other arrangement. Buyer will pay all damages awarded, and settlements approved by Buyer, in connection therewith, provided that (i) PacBio provides to Buyer written notice of the Claim within thirty (30) days of receipt by PacBio of such Claim, or such earlier time as required to avoid prejudice to Buyer or its ability to defend such Claim, (ii) PacBio allows Buyer to control the defense and settlement of the Claim, and (iii) PacBio provides to Buyer reasonable assistance in connection therewith, at no charge to Buyer. PacBio may employ counsel at its own expense to assist it with respect to any such Claim, provided that this shall not obligate Buyer or its counsel to consult with or advise such PacBio counsel, nor affect Buyer's control of the defense and settlement of the Claim. If Buyer is a U.S. state, city, town or other municipality, or a public university, college or other not-for-profit institution chartered under the laws of a U.S. state, this section shall apply to the maximum extent permitted by applicable law. This section shall not apply if Buyer is an agency of the U.S. Government; in such case, Buyer's liability shall be limited by the Federal Tort Claims Act, 28 USC 2671, et seq.
10.6 Insurance. To the extent Buyer's Terms (if applicable) require PacBio to maintain insurance coverage beyond the following levels, then such additional or different insurance terms shall be void and of no effect: (i) $1,000,000/$2,000,000 per occurrence/aggregate commercial general liability; (ii) $1,000,000 per accident combined single limit automobile liability; (iii) $4,000,000 per occurrence/aggregate excess/umbrella liability; and (iv) statutory workers' compensation and $1,000,000 per accident of employers' liability insurance. If requested in writing by Buyer, PacBio shall provide Buyer with a certificate of insurance evidencing the coverage required above, naming the Buyer as an additional insured only under PacBio's commercial general liability insurance policy, and providing for thirty (30) days' prior written notice to Buyer only in the event of cancellation and non-renewal of any such policy.
11. BUYER IMPROVEMENT PATENTS. Buyer agrees to make available to PacBio, under commercially reasonable and non-discriminatory pricing and terms, a nonexclusive license to Product Improvement Patents. For this purpose, "Product Improvement Patents" means all patent rights (including similar rights like utility models) on inventions conceived or reduced to practice by or for Buyer that arise out of the use of Products and which relate to (a) use, development, design, manufacturing, layout or packaging of any Products, and/or the use of Products with PacBio Consumables or other chips and/or reagents; (b) interfaces between any Products and other devices, such as optical/detection systems, and robotics for use in connection with any Products; or (c) automated analysis techniques (e.g., computers, software) relating to the extraction of data from any Products and storing such data, for example, in a computer file or other storage media (such inventions, "Product Improvement Inventions"). Product Improvement Inventions shall not include data resulting from using Products (e.g., results of assays or sequencing using Products) or discoveries derived from such data (except to the extent covered by (a), (b) or (c) above). For purposes of this section, the term "Buyer" shall include all persons that Buyer permits to use the Products, irrespective of being legal employees of Buyer, and Buyer shall have the necessary agreements in effect with all such users and their employers to enable Buyer to comply with this section.
12. MISCELLANEOUS
12.1 Notices. All notices and other communications required or permitted hereunder shall be in writing and shall be mailed by first class mail (registered or certified if available; air mail if overseas), postage prepaid, or otherwise delivered by hand, commercial courier service, messenger or telecopy, addressed to the addresses listed in the Quotation (or to Buyer's address listed in its purchase order) or at such other address furnished with a notice in the manner set forth herein. Such notices shall be deemed to have been effective when delivered or, if delivery is not accomplished by reason of some fault or refusal of the addressee, when tendered (which tender, in the case of mail, shall be deemed to have occurred upon posting, and in the case of telecopy (fax), shall be deemed to have occurred upon transmission). All notices shall be in English.
12.2 Governing Law and Venue. This Agreement and any disputes arising out of or relating do this Agreement (including its formation or termination) or PacBio's goods, software or related services ("Disputes") shall be governed by and interpreted in accordance with the laws of the State of California, U.S.A., (provided, however, that if Buyer is a U.S. state, city, town or other municipality, or a public university, college or other not-for-profit institution chartered under the laws of a U.S. state, the law of such state shall govern), excluding in all cases choice of law provisions and excluding the United Nations Convention on Contracts for the International Sale of Goods. If Buyer is located within the U.S., any Disputes may be brought in the state courts located in Santa Clara County, California or the U.S. District Court for the Northern District California, and each party consents to the personal and non-exclusive jurisdiction and venue of these courts. If Buyer is located outside the U.S., any Disputes shall be resolved by final and binding arbitration under the rules and auspices of the International Centre for Dispute Resolution in Santa Clara County, California, in English language proceedings whereby either party can request a written opinion from the arbitrator(s) appointed in accordance with the rules, which shall award legal fees (including reasonable attorneys' fees) to the party winning the proceedings, provided however, that either party may seek injunctive relief (including preliminary and permanent injunctive relief) before any court of competent jurisdiction. Any specification in Buyer's Terms (if applicable) of a different legal forum or venue for resolution of disputes between the parties shall be deemed non-exclusive, notwithstanding any provision in Buyer's Terms to the contrary. This section shall not apply if Buyer is an agency of the U.S. Government.
12.3 Purchases for the U.S. Government. If Buyer is placing an Order for the United States Government or in support of a contract with the U.S. Government, Buyer agrees that the Products purchased are "commercial items" as defined in the U.S. Federal Acquisition Regulations ("FAR"). If Buyer is placing this Order in the name of the U.S. Government and the Order is less than or equal to $3,000, then Buyer agrees that only these Terms shall apply to the Order. If the Order is greater than $3,000, then Buyer agrees that the Order is subject to FAR Part 12, and pursuant to FAR 12.301 and 12.302, only those mandatory provisions of FAR 52.212-1, 52.212-3, 52.212-4 and 52.212-5, and these Terms, shall apply. If Buyer is placing this Order in support of a contract with the U.S. Government, Buyer agrees that only those mandatory clauses listed in FAR 52.244-6 as well as these Terms shall apply to the Order. All other terms and conditions are expressly rejected. In the event of a conflict between the FAR provisions referenced herein and these Terms, these Terms shall take precedence to the maximum extent permitted by applicable law.
12.4 U.S. Government End Users. The Licensed Software and Documentation provided by PacBio pursuant to this Agreement are "commercial items," as the term is defined at 48 C.F.R. §2.101, consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. §12.212 or 48 C.F.R. §227.7202, as applicable. Consistent with 48 C.F.R. §12.212 or 48 C.F.R. §§227.7202-1 through 227.7202-4, as applicable, the commercial computer software and commercial computer software documentation are licensed to United States Government end users (i) only as commercial items and (ii) with only those rights granted pursuant to the terms of this Agreement.
12.5 Inspections; Access to Records. To the extent Buyer's Terms (if applicable) permit the inspection by or on behalf of Buyer of the Product(s) or PacBio's work and activities pursuant to Buyer's purchase order, or the examination or audit of PacBio's books and records, any such inspection, examination or audit shall be conducted at Buyer's sole expense by an independent auditor from a reputable public accounting firm duly authorized by Buyer, under reasonable obligations of confidentiality, and only during PacBio's normal business hours.
12.6 Export Controls. Buyer agrees that it will not export or transfer Product for re-export in violation of any United States laws or the laws of any other jurisdiction, or to any denied or prohibited person, entity, or embargoed country in violation of such laws.
12.7 Severability. If any section, paragraph, provision or clause or any portion thereof in this Agreement shall be found or be held to be invalid or unenforceable in any jurisdiction in which this Agreement is being performed, the remainder of this Agreement shall be valid and enforceable and the parties shall negotiate, in good faith, a substitute, valid and enforceable provision which most nearly effects the parties' intent in entering into this Agreement.
12.8 Force Majeure. Except for the payment of money, neither party shall be liable to the other party for any failure or delay in the performance of any of its obligations under this Agreement for the period and to the extent such failure or delay is caused by civil unrest, threat of or actual acts of terrorism or war, embargoes, governmental actions, acts of God, earthquakes, floods, storms, fires, supplier delay, accidents, explosions, epidemics, quarantine restrictions, or other such contingencies beyond the reasonable control of the applicable party ("Force Majeure"). The party affected shall notify the other party as soon as practicable of any anticipated delay due to Force Majeure.
12.9 No Third Party Beneficiaries. This Agreement has been made and is made solely for the benefit of PacBio and Buyer and their respective permitted Subsidiaries, successors and assigns. Except as set forth in Section 8.2 (with respect to Suppliers), nothing in this Agreement is intended to (i) confer any rights or remedies under or by reason of this Agreement on any persons or entity other than the parties to this Agreement and their respective permitted successors and assigns; or (ii) relieve or discharge the obligation or liability of any third persons or entities to any party to this Agreement.
12.10 General. The section headings contained in this Agreement are for reference purposes only and shall not affect in any way the meaning or interpretation of this Agreement. The English language shall govern the meaning and interpretation of this Agreement. This Agreement (including without limitation all exhibits hereto and all attachments thereto, which are incorporated herein by this reference as though fully set forth in the body of this Agreement) embodies the final and complete understanding of the parties with respect to the subject matter hereof, superseding all prior oral or written communications between them, and neither of the parties shall be bound by any conditions, definitions, warranties, understandings, or representations with respect to the subject matter hereof other than as expressly provided herein. Each party acknowledges that it has not entered into this Agreement in reliance on any statement or representation not expressly set out herein. No oral explanation or oral information by either party hereto shall alter the meaning or interpretation of this Agreement.
SOFTWARE END USER LICENSE AGREEMENT
These license terms are part of the agreement ("Agreement") between Pacific Biosciences of California, Inc. or its subsidiary ("PacBio"), and you (the "Licensee"). They apply to the software that accompanies these license terms, which includes the media on which you received it, if any. BY USING THE SOFTWARE, YOU ACCEPT THESE TERMS. PacBio does not accept, and PacBio expressly rejects hereby any conflicting or additional terms presented by Licensee, and such terms shall have no effect, whether or not PacBio communicates the rejection again specifically after receipt of Licensee's terms. The Agreement only consists of these terms and any other terms that PacBio issues or expressly accepts in a duly signed writing.
1. CERTAIN DEFINITIONS AND RELATED MATTERS
1.1 "Product" means each item, including any PacBio Instrument, Licensed Software and/or PacBio Consumable, listed in the applicable written sales quotation issued by PacBio ("Quotation"), or in the event a Quotation is not issued, listed in PacBio's then-current price list applicable to Licensee's jurisdiction, and rightfully obtained by Licensee from PacBio or its authorized distributor.
1.2 "PacBio Instrument" means a PacBio-branded instrument (including any PacBio® RS sequencing instrument).
1.3 "PacBio Consumables" means PacBio SMRT® Cells and/or associated PacBio-branded reagent kits, and labware intended by PacBio for use with PacBio Instruments.
1.4 "Licensed Software" means the (i) PacBio Instrument operating system software and firmware, including PacBio Instrument control, data collection and the PacBio Instrument's touch screen user interface ("O/S Software") and (ii) primary analysis software, including signal processing, base calling and quality assessment functions ("Primary Analysis Software"), in each case provided by PacBio to Licensee pre-installed on, and/or on DVD or other media delivered with, a PacBio Instrument unit and/or made available by PacBio for download, in object code or executable form only.
1.5 "Documentation" means the user documentation accompanying, or provided by PacBio regarding or for use in connection with a Product or related service.
1.6 "Other Software" means (i) any PacBio software or firmware, other than the Licensed Software, that PacBio makes available for use with PacBio Instruments or otherwise (e.g., alignment/assembly and consensus calling functions), and (ii) any third party software or firmware. "Other Software" may include open source software.
1.7 "Other License Terms" means, with respect to any Other Software, all of the terms, conditions and use restrictions set forth in the end user license agreement(s) and/or documentation accompanying and/or applicable to such Other Software.
2. LICENSE AND USE RESTRICTIONS
2.1 Limited License. Subject to the terms and conditions of this Agreement and, with respect to Other Software, to the applicable Other License Terms, PacBio grants to Licensee a non-exclusive, non-transferable, non-sublicensable license to use the Licensed Software and Documentation in connection with other Products in accordance with the applicable, then-current Documentation. PacBio hereby reserves all rights to the Licensed Software and Documentation, except for the rights expressly granted herein. No other license or authorization is granted, by implication, estoppel, or otherwise. For example, and without limiting the preceding sentence, no right or license is granted or implied, and Licensee is not authorized, to use any Product in combination with any product or method not provided, licensed or specifically recommend in writing by PacBio for such use.
2.2 Title. Licensee acknowledges that PacBio retains title to the Licensed Software and Documentation and each copy thereof provided to or made by Licensee, which copies are licensed to Licensee for use in accordance with this Agreement. PacBio only licenses Software and Documentation. PacBio never sells Software or Documentation or copies thereof.
2.3 Copies. Licensee may make a single machine-readable copy of the Licensed Software for backup or archival purposes. Licensee may make a reasonable number of copies of the Documentation in support of its use of the Licensed Software pursuant to this Agreement. Licensee shall not make any other copies of the Licensed Software or Documentation. Licensee shall maintain accurate and up to date records of the number and location of all copies of the Licensed Software and Documentation and, upon request, inform PacBio in writing of such location. All copies of the Licensed Software and Documentation will be subject to the terms and conditions of this Agreement. On each copy Licensee shall reproduce, and shall not modify, obscure, or efface, any and all titles, trademark symbols, copyright symbols, notices and legends, and other proprietary markings on or in the Licensed Software and Documentation.
2.4 No Source Code. Licensee is granted no rights with respect to the Licensed Software source code. Licensee is granted no rights to, and Licensee agrees that it will not, and will not authorize or permit any third party to, decompile, disassemble, or reverse engineer, or attempt to derive the source code for the Licensed Software, in whole or in part.
2.5 Other Restrictions. Licensee shall not, and shall not authorize or permit any third party to: (a) sell, lease, license, sublicense, or otherwise transfer the Licensed Software or the Documentation; (b) provide, disclose, or make the Licensed Software or Documentation available to any third party, or permit access to or use of the Licensed Software or Documentation by any person other than Licensee's employees, agents, or contractors who are, by agreement, bound by the terms of this Agreement to the same extent as Licensee; (c) merge or combine the Licensed Software with other software, or modify the Licensed Software, or create any derivative software or any other software based upon, or any derivative work of, the Licensed Software or Documentation; or (d) modify or efface any titles, trademark symbols, copyright symbols, notices or legends, or any other proprietary markings on or in the Licensed Software or Documentation. All license restrictions specified in Sections 2.4 and 2.5 and elsewhere in the Agreement shall apply to the maximum extent permissible under applicable law. If Licensee believes that it has additional rights or the right to act contrary to the express license restrictions specified in this Agreement under mandatory laws (including, without limitation, national laws implementing Directive 91/250/EEC and similar laws), Licensee agrees that it shall provide PacBio with at least 30 days prior written notice and any reasonably requested information before exercising such rights, to allow PacBio to offer alternatives at PacBio's sole discretion, for example interface information to achieve interoperability with independently created computer programs.
2.6 Regulatory Compliance. Licensee acknowledges that the Licensed Software does not have United States Food and Drug Administration ("FDA") or equivalent non-U.S. regulatory agency approval ("Approval"). Accordingly, Licensee acknowledges that the Licensed Software is intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES. The Licensed Software should be used by qualified professionals in strict accordance with applicable instructions, warnings and other information in user manuals and other Documentation. Unless otherwise expressly stated by PacBio in writing, no claim or representation is made or intended by PacBio (i) as to any diagnostic or other clinical use of the Licensed Software; (ii) that any Licensed Software has any Approval for use in any diagnostic or other clinical procedure, or for any other use requiring compliance with any law, regulation or governmental policy concerning medical devices, laboratory tests or the like (collectively, "Regulatory Laws"); (iii) that any Licensed Software will satisfy the requirements of the FDA or any other regulatory agency; or (iv) that any Licensed Software or its performance is suitable or has been validated for clinical or diagnostic use, for safety and effectiveness, for any specific use or application, or for importation into Licensee's jurisdiction. Licensee agrees that if it elects to use the Licensed Software for a purpose that would subject Licensee, its customers or any Product to the application of Regulatory Laws or any other law, regulation or governmental policy, Licensee shall be solely responsible for obtaining any required Approvals and otherwise ensuring that the importation of the Products into Licensee's jurisdiction and Licensee's use of Products complies with all such laws, regulations and policies. The burden of proof for safe use and handling of the Licensed Software is entirely the responsibility of Licensee.
2.7 U.S. Government End Users. The Licensed Software and Documentation provided by PacBio pursuant to this Agreement are "commercial items," as the term is defined at 48 C.F.R. §2.101, consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. §12.212 or 48 C.F.R. §227.7202, as applicable. Consistent with 48 C.F.R. §12.212 or 48 C.F.R. §§227.7202-1 through 227.7202-4, as applicable, the commercial computer software and commercial computer software documentation are licensed to United States Government end users (i) only as commercial items and (ii) with only those rights as are granted pursuant to the terms of this Agreement.
2.8 Other Software and Other License Terms. The Licensed Software may contain, be accompanied by and/or be intended by PacBio to interact with, Other Software, which is provided under separate Other License Terms. Such Other Software and/or the applicable Other License Terms may be listed or identified in the Licensed Software or Documentation or contained in a file or directory provided with the delivery of the Licensed Software. Licensee's use of such Other Software in conjunction with the Licensed Software in a manner consistent with the terms of this Agreement is permitted. However, the Licensee may have broader rights with respect to the Other Software under the applicable Other License Terms and nothing in this Agreement is intended to impose further restrictions on the Licensee's use of such Other Software.
3. NO STANDALONE WARRANTY; LIABILITY LIMITATIONS AND DISCLAIMERS
3.1 No Standalone Warranty for Licensed Software. PacBio's product warranty for each PacBio Instrument (including its use in connection with the most current version of Licensed Software, or, with PacBio approval, a previous version of the Licensed Software) is included with shipment of such PacBio Instrument, or can be obtained directly by contacting PacBio. PacBio makes no standalone warranty with regard to Licensed Software. CONSEQUENTLY, THE LICENSED SOFTWARE (AND ANY OTHER SOFTWARE) IS PROVIDED BY PACBIO "AS-IS" WITHOUT (AND PACBIO HEREBY DISCLAIMS) ANY WARRANTY, STATUTORY, EXPRESS OR IMPLIED. PacBio may, at Licensee's request, furnish technical assistance, advice and information with respect to the Licensed Software (beyond the scope of PacBio's applicable product warranty or service contract for the PacBio Instrument(s) used by Licensee in connection with the Licensed Software). It is expressly agreed that there is no obligation to provide such assistance, advice or information, which are provided "AS IS," without additional charge, and at Licensee's sole risk.
3.2 Disclaimer; No Other Warranties. ANY WARRANTY PROVIDED IN CONNECTION WITH THE PACBIO INSTRUMENT(S) USED BY LICENSEE IN CONNECTION WITH THE LICENSED SOFTWARE AND/OR OTHER SOFTWARE (AND ANY REMEDY THEREIN PROVIDED) ARE IN LIEU OF, AND PACBIO HEREBY DISCLAIMS, ALL REMEDIES AND WARRANTIES, EXPRESS, STATUTORY, IMPLIED, OR OTHERWISE, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NONINFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE, OR REGARDING RESULTS OBTAINED THROUGH THE USE OF THE LICENSED SOFTWARE AND/OR OTHER SOFTWARE (INCLUDING, WITHOUT LIMITATION, ANY CLAIM OF INACCURATE, INVALID OR INCOMPLETE RESULTS), IN EACH CASE HOWEVER ARISING, INCLUDING WITHOUT LIMITATION FROM A COURSE OF PERFORMANCE, DEALING OR USAGE OF TRADE, OR OTHERWISE. IN NO EVENT SHALL PACBIO BE LIABLE FOR COSTS OF SUBSTITUTE GOODS OR SERVICES, OR FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR INDIRECT DAMAGES FOR BREACH OF WARRANTY.
3.3 Limitation of Liability. EXCEPT AS OTHERWISE EXPRESSLY AGREED BY PACBIO IN WRITING, PACBIO'S LIABILITY ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, THE LICENSED SOFTWARE AND/OR OTHER SOFTWARE SHALL BE LIMITED TO THE AMOUNT PAID (IF ANY) BY THE LICENSEE FOR THE LICENSED SOFTWARE AND/OR OTHER SOFTWARE GIVING RISE TO THE LIABILITY, OR ONE HUNDRED UNITED STATES DOLLARS (US$100.00), WHICHEVER IS GREATER, AND IN NO EVENT SHALL PACBIO'S AGGREGATE LIABILITY ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, THE LICENSED SOFTWARE AND/OR OTHER SOFTWARE EXCEED THE TOTAL AMOUNTS RECEIVED BY PACBIO UNDER THE APPLICABLE AGREEMENT(S) WITH PACBIO GOVERNING LICENSEE'S PURCHASE OF THE PACBIO INSTRUMENT(S) WITH WHICH THE LICENSED SOFTWARE IS USED BY LICENSEE. IN NO EVENT SHALL PACBIO BE LIABLE FOR COSTS OF SUBSTITUTE GOODS OR SERVICES, OR FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR INDIRECT DAMAGES, HOWEVER CAUSED AND UNDER ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, TORT, WARRANTY, PURSUANT TO ANY STATUTE, OR ON ANY OTHER BASIS, ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, THE LICENSED SOFTWARE, OTHER SOFTWARE AND/OR SALE OF THE PRODUCTS OR SERVICES , WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT PACBIO IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS OF USE, LOSS OF DATA, OR DOWNTIME, OR FOR LOSS OF REVENUE OR PROFITS. THESE LIMITATIONS SHALL APPLY NOTWITHSTANDING ANY FAILURE OF ESSENTIAL PURPOSE OF ANY LIMITED REMEDY.
3.4 Third Party Disclaimers. Unless otherwise expressly indicated in the Quotation, Documentation or any Other License Terms, none of PacBio's suppliers or licensors of any Product or other item provided by PacBio, or portion thereof (under this Agreement or otherwise) (each, a "Supplier") provides ANY WARRANTY WHATSOEVER, EXPRESS, STATUTORY, IMPLIED, OR OTHERWISE, TO LICENSEE, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NONINFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE, AND ALL SUCH WARRANTIES ARE DISCLAIMED. IN NO EVENT SHALL ANY SUPPLIER BE LIABLE TO LICENSEE FOR ANY SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY, DIRECT, INDIRECT OR OTHER DAMAGES ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT OR THE PRODUCTS.
3.5 Indemnification of PacBio. Licensee agrees to defend PacBio against any third party claim, proceeding or action ("Claim") that arises in connection with Licensee's use of the Licensed Software (a) for any clinical purpose or application, (b) in violation of any applicable law or regulation, or (c) in the provision of services under any 'fee for service' agreement or other arrangement. Licensee will pay all damages awarded, and settlements approved by Licensee, in connection therewith, provided that (i) PacBio provides to Licensee written notice of the Claim within thirty (30) days of receipt by PacBio of such Claim, (ii) PacBio allows Licensee to control the defense and settlement of the Claim, and (iii) PacBio provides to Licensee reasonable assistance in connection therewith, at no charge to Licensee. PacBio may employ counsel at its own expense to assist it with respect to any such Claim, provided that this shall not obligate Licensee or its counsel to consult with or advise such PacBio counsel, nor affect Licensee's control of the defense and settlement of the Claim.
4. MISCELLANEOUS
4.1 Notices. All notices and other communications required or permitted hereunder shall be in writing and shall be mailed by first class mail (registered or certified if available; air mail if overseas), postage prepaid, or otherwise delivered by hand, commercial courier service, messenger or telecopy, addressed to the addresses first set forth above or at such other address furnished with a notice in the manner set forth herein. Such notices shall be deemed to have been effective when delivered or, if delivery is not accomplished by reason of some fault or refusal of the addressee, when tendered (which tender, in the case of mail, shall be deemed to have occurred upon posting, and in the case of telecopy (fax), shall be deemed to have occurred upon transmission). All notices shall be in English.
4.2 Governing Law and Venue. This Agreement and any disputes arising out of or relating do this Agreement (including its formation or termination) or PacBio's goods, software or related services ("Disputes") shall be governed by and interpreted in accordance with the laws of the State of California, U.S.A., excluding in all cases choice of law provisions and excluding the United Nations Convention on Contracts for the International Sale of Goods. If Licensee is located within the U.S., any Disputes may be brought in the state courts located in Santa Clara County, California or the U.S. District Court for the Northern District of California, and each party consents to the personal and non-exclusive jurisdiction and venue of these courts. If Licensee is located outside the U.S., any Disputes shall be resolved by final and binding arbitration under the rules and auspices of the International Centre for Dispute Resolution in Santa Clara County, California, in English language proceedings whereby either party can request a written opinion from the arbitrator(s) appointed in accordance with the rules, which shall award legal fees (including reasonable attorneys' fees) to the party winning the proceedings, provided however, that either party may seek injunctive relief (including preliminary and permanent injunctive relief) before any court of competent jurisdiction. This section shall not apply if Licensee is an agency of the U.S. Government.
4.3 Export Controls. Licensee agrees that it will not export or transfer the Licensed Software or Documentation for re-export in violation of any United States laws or the laws of any other jurisdiction, or to any denied or prohibited person, entity, or embargoed country in violation of such laws.
4.4 Severability. If any section, paragraph, provision or clause or any portion thereof in this Agreement shall be found or be held to be invalid or unenforceable in any jurisdiction in which this Agreement is being performed, the remainder of this Agreement shall be valid and enforceable and the parties shall negotiate, in good faith, a substitute, valid and enforceable provision which most nearly effects the parties' intent in entering into this Agreement.
4.5 Force Majeure. Neither party shall be liable to the other party for any failure or delay in the performance of any of its obligations under this Agreement for the period and to the extent such failure or delay is caused by civil unrest, threat of or actual acts of terrorism or war, embargoes, governmental actions, acts of God, earthquakes, floods, storms, fires, supplier delay , accidents, explosions, epidemics, quarantine restrictions, or other such contingencies beyond the reasonable control of the applicable party ("Force Majeure"). The party affected shall notify the other party as soon as practicable of any anticipated delay due to Force Majeure.
4.6 No Third Party Beneficiaries. This Agreement has been made and is made solely for the benefit of PacBio and Licensee and their respective permitted subsidiaries, successors and assigns. Except as set forth in Section 3.4 (with respect to Suppliers), nothing in this Agreement is intended to confer any rights or remedies under or by reason of this Agreement on any persons or entity other than the parties to this Agreement and their respective permitted successors and assigns, or relieve or discharge the obligation or liability of any third persons or entities to any party to this Agreement.
4.7 General. The section headings contained in this Agreement are for reference purposes only and shall not affect in any way the meaning or interpretation of this Agreement. The English language shall govern the meaning and interpretation of this Agreement. This Agreement (including without limitation all exhibits hereto and all attachments thereto, which are incorporated herein by this reference as though fully set forth in the body of this Agreement) embodies the final and complete understanding of the parties with respect to the subject matter hereof, superseding all prior oral or written communications between them, and neither of the parties shall be bound by any conditions, definitions, warranties, understandings, or representations with respect to the subject matter hereof other than as expressly provided herein. Each party acknowledges that it has not entered into this Agreement in reliance on any statement or representation not expressly set out herein. No oral explanation or oral information by either party hereto shall alter the meaning or interpretation of this Agreement.
(57) IPRSCAN
InterProScan FTP site
Version 4.4
This is the FTP site for downloading InterProScan. During a typical installation you will need the following files:
Documentation
README giving a quick overview of how to use InterProScan and what the program actually does
Frequently Asked Questions for both the administrators and users (updated 28th May 2008)
Installation Instructions in txt format, should you wish to download InterProScan to your own server
Release Notes for the latest version of the software - what's new and what is coming soon.
Data Release Notes for the latest release of the data - which files have updated, etc.
Binary Release Notes for the latest release of the software.
Files on this site
ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/DATA/ Contains database files (3 tarballs) - currently v18.0, released 1st September 2008
Please download all 3 files and install as per the Installation Instructions:
latest_pthr: Latest release of Panther data
latest_no_pthr: Latest release of other member database files (not Panther)
latest_match: Latest versions of match_complete.xml and interpro.xml files and their DTDs
ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/ Contains binaries pre-compiled for various OS. Please read the README for important information about FingerPRINTScan in v4.4
ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/RELEASE/latest/ Contains InterProScan itself (perl architecture) - currently v4.4, released 4th September 2008.
Please note that all files must be downloaded before Config.pl is run to do the installation.
Inter-release patches
Please check the PATCHES directory for patches and quick bug-fixes discovered since release. These will also be listed below, together with any changes required to the installation
The table below list patches since v4.4.
Date File Instructions
4th Sep 2008
InterProScan 4.4 released
Apologies for any inconvenience these bugs may have caused
Copyright: © EMBL-EBI 2008
(58) OrthoMCL
The OrthoMCL Software is Copyright 2010 by the EuPathDB Bioinformatics Resource Center.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
(59) TribeMCL
#!/usr/bin/env perl
# Copyright (C) 2002, EMBL-EBI, author Anton Enright. #
# #
# This file is part of MCL. You can redistribute and/or modify MCL under the #
# terms of the GNU General Public License; either version 2 of the License or #
# (at your option) any later version. You should have received a copy of the #
# GPL along with MCL, in the file COPYING. #
#
# $Id: tribemcl,v 1.6 2003/05/25 20:29:13 flux Exp $
#
# tribemcl -> A Wrapper Script for performing a TRIBEMCL clustering
# for a set of BLASTp 2.0 protein sequence similarity results
#
# Anton Enright - EMBL-EBI 2002
$starttime=time();
@directory=split("/",$0);
splice(@directory,-1,1);
$directory=join("/",@directory);
if (!$directory)
{
$directory=`pwd`;
chop($directory);
}
$|=1;
$Inflation=3.0;
system("clear");
print " ###################################################################### \n";
print "# TRIBE-MCL #\n";
print "# #\n";
print "# An efficient algorithm for large-scale detection of protein families #\n";
print " ######################################################################\n";
print "Please Cite:\n";
print "------------\n";
print "Enright A.J., Van Dongen S., Ouzounis C.A;\n";
print "Nucleic Acids Res. 30(7):1575-1584 (2002)\n\n";
print "Please Cite:\n";
print "------------\n";
print "Stijn van Dongen, Graph Clustering by Flow Simulation,\n";
print "PhD thesis, University of Utrecht, May 2000.\n";
print "-- OR ------\n";
print "Stijn van Dongen, A cluster algorithm for graphs. Technical\n";
print "Report INS-R0010, National Research Institute for Mathematics\n";
print "and Computer Science in the Netherlands, Amsterdam, May 2000.\n\n";
for ($i=0;$i<$#ARGV+1;$i++)
{
if ($ARGV[$i] eq '-h')
{
print "This wrapper script is for starting an MCL clustering analysis\non protein sequence similarity data obtained with BLAST\n";
print "\n";
print "Prerequisites:\n";
print "--------------\n";
print "A standard NCBI BLASTp v2.0 output file from an all\n";
print "against all comparison of a set of protein sequences\n";
print "\n";
print "Usage:\n";
print "------\n";
print "tribemcl someblastresults.out\n";
print "\n";
print "Options:\n";
print "--------\n";
print "-h -> Print this help message\n";
print "-I X -> Where X is an inflation value greater than 1.0 \n";
print " (Default X=3.0)\n";
print "\n\n";
exit(1);
}
if (($ARGV[$i] eq '-I') && ($ARGV[$i+1]>0))
{
print "Changing Inflation Parameter to $ARGV[$i+1]\n";
$Inflation=$ARGV[$i+1];
}
}
if (!$ARGV[0])
{
print "Error: Please specify a filename to cluster\n";
exit(0);
}
$filename=(split("/",$ARGV[0]))[-1];
print "\nParsing BLAST similarities: ";
if(system ("$directory/tribe-parse $ARGV[0] > $filename.mclparsed"))
{
print "TRIBE-MCL Fatal Error (parsing)\n";
exit(1);
}
print "done\n\nGenerating Markov Matrix: ";
if(system("$directory/tribe-matrix $filename.mclparsed -ind $filename.index -out $filename.mci > /dev/null"))
{
print "TRIBE-MCL Fatal Error (matrix construction)\n";
exit(1);
}
print "done\n\nCalling MCL Cluster Algorithm: ";
if(system("$directory/mcl $filename.mci -I $Inflation -progress 100 -o $filename.mclout"))
{
print "TRIBE-MCL Fatal Error (markov clustering)\n";
exit(1);
}
print "done\n\nCollating Results: ";
if(system("$directory/tribe-families $filename.mclout $filename.index> $filename.mclclusters"))
{
print "TRIBE-MCL Fatal Error (result parsing)\n";
exit(1);
}
print "done\n\nCreated Clusters File $filename.mclclusters\n";
print "\n----------------------------------------------------------------------------\n";
print "Run Completed in ",time()-$starttime," seconds\n";
(60) MOCAT
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy. The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.
A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
1. Source Code.
The "source code" for a work means the preferred form of the work
for making modifications to it. "Object code" means any non-source
form of a work.
A "Standard Interface" means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that
is widely used among developers working in that language.
The "System Libraries" of an executable work include anything, other
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
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Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
(61) Qiime
Copyright for “qiime” source package in Precise
Ubuntu
Precise (12.04)
“qiime” source package
Copyright
This work was packaged for Debian by:
Sri Girish Srinivasa Murthy
and Steffen Moeller
on Fri, 25 Jun 2010 17:23:58 +0200
It was downloaded from
Upstream Author:
Greg Caporaso
Kyle Bittinger
Copyright:
Copyright 2010, The QIIME Project
License:
GPL-2
The Debian packaging is:
Copyright (C) 2010 Sri Girish Srinivasa Murthy
and Steffen Moeller
and is licensed under the same copyright,
see `/usr/share/common-licenses/GPL-2'.
(62) Circos
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for software and other kinds of works.
The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
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The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS
0. Definitions.
“This License” refers to version 3 of the GNU General Public License.
“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
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An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
1. Source Code.
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A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.
The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
The Corresponding Source for a work in source code form is that same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
3. Protecting Users' Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:
a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”.
c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.
A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.
“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
7. Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.
All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
11. Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see .
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read .
(63) Biopieces
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.
Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.
You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.
c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.
In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.
3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.
5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License.
7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.
10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
one line to give the program's name and an idea of what it does.
Copyright (C) yyyy name of author
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details
type `show w'. This is free software, and you are welcome
to redistribute it under certain conditions; type `show c'
for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright
interest in the program `Gnomovision'
(which makes passes at compilers) written
by James Hacker.
signature of Ty Coon, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License.
(64) MAKER
Artistic License 2.0
Copyright (c) 2000-2006, The Perl Foundation.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software.
You are always permitted to make arrangements wholly outside of this license directly with the Copyright Holder of a given Package. If the terms of this license do not permit the full use that you propose to make of the Package, you should contact the Copyright Holder and seek a different licensing arrangement.
Definitions
"Copyright Holder" means the individual(s) or organization(s) named in the copyright notice for the entire Package.
"Contributor" means any party that has contributed code or other material to the Package, in accordance with the Copyright Holder's procedures.
"You" and "your" means any person who would like to copy, distribute, or modify the Package.
"Package" means the collection of files distributed by the Copyright Holder, and derivatives of that collection and/or of those files. A given Package may consist of either the Standard Version, or a Modified Version.
"Distribute" means providing a copy of the Package or making it accessible to anyone else, or in the case of a company or organization, to others outside of your company or organization.
"Distributor Fee" means any fee that you charge for Distributing this Package or providing support for this Package to another party. It does not mean licensing fees.
"Standard Version" refers to the Package if it has not been modified, or has been modified only in ways explicitly requested by the Copyright Holder.
"Modified Version" means the Package, if it has been changed, and such changes were not explicitly requested by the Copyright Holder.
"Original License" means this Artistic License as Distributed with the Standard Version of the Package, in its current version or as it may be modified by The Perl Foundation in the future.
"Source" form means the source code, documentation source, and configuration files for the Package.
"Compiled" form means the compiled bytecode, object code, binary, or any other form resulting from mechanical transformation or translation of the Source form.
Permission for Use and Modification Without Distribution
(1) You are permitted to use the Standard Version and create and use Modified Versions for any purpose without restriction, provided that you do not Distribute the Modified Version.
Permissions for Redistribution of the Standard Version
(2) You may Distribute verbatim copies of the Source form of the Standard Version of this Package in any medium without restriction, either gratis or for a Distributor Fee, provided that you duplicate all of the original copyright notices and associated disclaimers. At your discretion, such verbatim copies may or may not include a Compiled form of the Package.
(3) You may apply any bug fixes, portability changes, and other modifications made available from the Copyright Holder. The resulting Package will still be considered the Standard Version, and as such will be subject to the Original License.
Distribution of Modified Versions of the Package as Source
(4) You may Distribute your Modified Version as Source (either gratis or for a Distributor Fee, and with or without a Compiled form of the Modified Version) provided that you clearly document how it differs from the Standard Version, including, but not limited to, documenting any non-standard features, executables, or modules, and provided that you do at least ONE of the following:
(a) make the Modified Version available to the Copyright Holder of the Standard Version, under the Original License, so that the Copyright Holder may include your modifications in the Standard Version.
(b) ensure that installation of your Modified Version does not prevent the user installing or running the Standard Version. In addition, the Modified Version must bear a name that is different from the name of the Standard Version.
(c) allow anyone who receives a copy of the Modified Version to make the Source form of the Modified Version available to others under
(i) the Original License or
(ii) a license that permits the licensee to freely copy, modify and redistribute the Modified Version using the same licensing terms that apply to the copy that the licensee received, and requires that the Source form of the Modified Version, and of any works derived from it, be made freely available in that license fees are prohibited but Distributor Fees are allowed.
Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source
(5) You may Distribute Compiled forms of the Standard Version without the Source, provided that you include complete instructions on how to get the Source of the Standard Version. Such instructions must be valid at the time of your distribution. If these instructions, at any time while you are carrying out such distribution, become invalid, you must provide new instructions on demand or cease further distribution. If you provide valid instructions or cease distribution within thirty days after you become aware that the instructions are invalid, then you do not forfeit any of your rights under this license.
(6) You may Distribute a Modified Version in Compiled form without the Source, provided that you comply with Section 4 with respect to the Source of the Modified Version.
Aggregating or Linking the Package
(7) You may aggregate the Package (either the Standard Version or Modified Version) with other packages and Distribute the resulting aggregation provided that you do not charge a licensing fee for the Package. Distributor Fees are permitted, and licensing fees for other components in the aggregation are permitted. The terms of this license apply to the use and Distribution of the Standard or Modified Versions as included in the aggregation.
(8) You are permitted to link Modified and Standard Versions with other works, to embed the Package in a larger work of your own, or to build stand-alone binary or bytecode versions of applications that include the Package, and Distribute the result without restriction, provided the result does not expose a direct interface to the Package.
Items That are Not Considered Part of a Modified Version
(9) Works (including, but not limited to, modules and scripts) that merely extend or make use of the Package, do not, by themselves, cause the Package to be a Modified Version. In addition, such works are not considered parts of the Package itself, and are not subject to the terms of this license.
General Provisions
(10) Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.
(11) If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.
(12) This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.
(13) This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.
(14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
(65) GRASS
GRASS License
The GRASS GIS project is developed under the terms of the GNU General Public License (the GPL) in the open by volunteers the world over.
How the Open Source software development model works
Wikipedia entry discussing the GPL
The Software Freedom Law Center's Legal Issues Primer for Open Source and Free Software Projects.
(66) IGV
The GNU Lesser General Public License, version 2.1 (LGPL-2.1)
[OSI Approved License]
GNU Lesser General Public License
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts as the successor of the GNU Library Public License, version 2, hence the version number 2.1.]
Preamble
The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public Licenses are intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users.
This license, the Lesser General Public License, applies to some specially designated software packages--typically libraries--of the Free Software Foundation and other authors who decide to use it. You can use it too, but we suggest you first think carefully about whether this license or the ordinary General Public License is the better strategy to use in any particular case, based on the explanations below.
When we speak of free software, we are referring to freedom of use, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish); that you receive source code or can get it if you want it; that you can change the software and use pieces of it in new free programs; and that you are informed that you can do these things.
To protect your rights, we need to make restrictions that forbid distributors to deny you these rights or to ask you to surrender these rights. These restrictions translate to certain responsibilities for you if you distribute copies of the library or if you modify it.
For example, if you distribute copies of the library, whether gratis or for a fee, you must give the recipients all the rights that we gave you. You must make sure that they, too, receive or can get the source code. If you link other code with the library, you must provide complete object files to the recipients, so that they can relink them with the library after making changes to the library and recompiling it. And you must show them these terms so they know their rights.
We protect your rights with a two-step method: (1) we copyright the library, and (2) we offer you this license, which gives you legal permission to copy, distribute and/or modify the library.
To protect each distributor, we want to make it very clear that there is no warranty for the free library. Also, if the library is modified by someone else and passed on, the recipients should know that what they have is not the original version, so that the original author's reputation will not be affected by problems that might be introduced by others.
Finally, software patents pose a constant threat to the existence of any free program. We wish to make sure that a company cannot effectively restrict the users of a free program by obtaining a restrictive license from a patent holder. Therefore, we insist that any patent license obtained for a version of the library must be consistent with the full freedom of use specified in this license.
Most GNU software, including some libraries, is covered by the ordinary GNU General Public License. This license, the GNU Lesser General Public License, applies to certain designated libraries, and is quite different from the ordinary General Public License. We use this license for certain libraries in order to permit linking those libraries into non-free programs.
When a program is linked with a library, whether statically or using a shared library, the combination of the two is legally speaking a combined work, a derivative of the original library. The ordinary General Public License therefore permits such linking only if the entire combination fits its criteria of freedom. The Lesser General Public License permits more lax criteria for linking other code with the library.
We call this license the "Lesser" General Public License because it does Less to protect the user's freedom than the ordinary General Public License. It also provides other free software developers Less of an advantage over competing non-free programs. These disadvantages are the reason we use the ordinary General Public License for many libraries. However, the Lesser license provides advantages in certain special circumstances.
For example, on rare occasions, there may be a special need to encourage the widest possible use of a certain library, so that it becomes a de-facto standard. To achieve this, non-free programs must be allowed to use the library. A more frequent case is that a free library does the same job as widely used non-free libraries. In this case, there is little to gain by limiting the free library to free software only, so we use the Lesser General Public License.
In other cases, permission to use a particular library in non-free programs enables a greater number of people to use a large body of free software. For example, permission to use the GNU C Library in non-free programs enables many more people to use the whole GNU operating system, as well as its variant, the GNU/Linux operating system.
Although the Lesser General Public License is Less protective of the users' freedom, it does ensure that the user of a program that is linked with the Library has the freedom and the wherewithal to run that program using a modified version of the Library.
The precise terms and conditions for copying, distribution and modification follow. Pay close attention to the difference between a "work based on the library" and a "work that uses the library". The former contains code derived from the library, whereas the latter must be combined with the library in order to run.
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other program which contains a notice placed by the copyright holder or other authorized party saying it may be distributed under the terms of this Lesser General Public License (also called "this License"). Each licensee is addressed as "you".
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This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
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NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest possible use to the public, we recommend making it free software that everyone can redistribute and change. You can do so by permitting redistribution under these terms (or, alternatively, under the terms of the ordinary General Public License).
To apply these terms, attach the following notices to the library. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the library, if necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the library `Frob' (a library for tweaking knobs) written by James Random Hacker.
signature of Ty Coon, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!
(67) Bowtie
The Artistic License
Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to
make reasonable modifications.
Definitions:
* "Package" refers to the collection of files distributed by the
Copyright Holder, and derivatives of that collection of files
created through textual modification.
* "Standard Version" refers to such a Package if it has not been
modified, or has been modified in accordance with the wishes of
the Copyright Holder.
* "Copyright Holder" is whoever is named in the copyright or
copyrights for the package.
* "You" is you, if you're thinking about copying or distributing
this Package.
* "Reasonable copying fee" is whatever you can justify on the
basis of media cost, duplication charges, time of people
involved, and so on. (You will not be required to justify it to
the Copyright Holder, but only to the computing community at
large as a market that must bear the fee.)
* "Freely Available" means that no fee is charged for the item
itself, though there may be fees involved in handling the
item. It also means that recipients of the item may redistribute
it under the same conditions they received it.
1. You may make and give away verbatim copies of the source form of
the Standard Version of this Package without restriction, provided
that you duplicate all of the original copyright notices and
associated disclaimers.
2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A
Package modified in such a way shall still be considered the
Standard Version.
3. You may otherwise modify your copy of this Package in any way,
provided that you insert a prominent notice in each changed file
stating how and when you changed that file, and provided that you
do at least ONE of the following:
a) place your modifications in the Public Domain or otherwise make
them Freely Available, such as by posting said modifications to
Usenet or an equivalent medium, or placing the modifications on a
major archive site such as ftp.uu.net, or by allowing the
Copyright Holder to include your modifications in the Standard
Version of the Package.
b) use the modified Package only within your corporation or
organization.
c) rename any non-standard executables so the names do not
conflict with standard executables, which must also be provided,
and provide a separate manual page for each non-standard
executable that clearly documents how it differs from the Standard
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d) make other distribution arrangements with the Copyright Holder.
4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the
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files, together with instructions (in the manual page or
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b) accompany the distribution with the machine-readable source of
the Package with your modifications.
c) accompany any non-standard executables with their corresponding
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non-standard names, and clearly documenting the differences in
manual pages (or equivalent), together with instructions on where
to get the Standard Version.
d) make other distribution arrangements with the Copyright Holder.
5. You may charge a reasonable copying fee for any distribution of
this Package. You may charge any fee you choose for support of this
Package. You may not charge a fee for this Package itself. However,
you may distribute this Package in aggregate with other (possibly
commercial) programs as part of a larger (possibly commercial)
software distribution provided that you do not advertise this
Package as a product of your own.
6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whomever
generated them, and may be sold commercially, and may be aggregated
with this Package.
7. C or perl subroutines supplied by you and linked into this Package
shall not be considered part of this Package.
8. The name of the Copyright Holder may not be used to endorse or
promote products derived from this software without specific prior
written permission.
9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
The End
This license is approved by the Open Source Initiative
(www.opensource.org) for certifying software as OSI Certified Open
Source.
(68) BWA
AUTHOR
Heng Li at the Sanger Institute wrote the key source codes and integrated the following codes for BWT construction: bwtsw , implemented by Chi-Kwong Wong at the University of Hong Kong and IS originally proposed by Nong Ge at the Sun Yat-Sen University and implemented by Yuta Mori.
LICENSE AND CITATION
The full BWA package is distributed under GPLv3 as it uses source codes from BWT-SW which is covered by GPL. Sorting, hash table, BWT and IS libraries are distributed under the MIT license.
If you use the BWA-backtrack algorithm, please cite the following paper:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
If you use the BWA-SW algorithm, please cite:
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]
If you use the fastmap component of BWA, please cite:
Li H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844. [PMID: 22569178]
The BWA-MEM algorithm has not been published yet.
HISTORY
BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW and mimics its binary file formats; BWA-SW resembles BWT-SW in several ways. The initial idea about BWT-based alignment also came from the group who developed BWT-SW. At the same time, BWA is different enough from BWT-SW. The short-read alignment algorithm bears no similarity to Smith-Waterman algorithm any more. While BWA-SW learns from BWT-SW, it introduces heuristics that can hardly be applied to the original algorithm. In all, BWA does not guarantee to find all local hits as what BWT-SW is designed to do, but it is much faster than BWT-SW on both short and long query sequences.
I started to write the first piece of codes on 24 May 2008 and got the initial stable version on 02 June 2008. During this period, I was acquainted that Professor Tak-Wah Lam, the first author of BWT-SW paper, was collaborating with Beijing Genomics Institute on SOAP2, the successor to SOAP (Short Oligonucleotide Analysis Package). SOAP2 has come out in November 2008. According to the SourceForge download page, the third BWT-based short read aligner, bowtie, was first released in August 2008. At the time of writing this manual, at least three more BWT-based short-read aligners are being implemented.
The BWA-SW algorithm is a new component of BWA. It was conceived in November 2008 and implemented ten months later.
The BWA-MEM algorithm is based on an algorithm finding super-maximal exact matches (SMEMs), which was first published with the fermi assembler paper in 2012. I first implemented the basic SMEM algorithm in the fastmap command for an experiment and then extended the basic algorithm and added the extension part in Feburary 2013 to make BWA-MEM a fully featured mapper.
(69) Cufflinks
Copyright (C) 2003-2009 Cole Trapnell et al
===========================================================================
Boost Software License, Version 1.0
===========================================================================
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (the "Software") to use, reproduce, display, distribute,
execute, and transmit the Software, and to prepare derivative works of the
Software, and to permit third-parties to whom the Software is furnished to
do so, all subject to the following:
The copyright notices in the Software and this entire statement, including
the above license grant, this restriction and the following disclaimer,
must be included in all copies of the Software, in whole or in part, and
all derivative works of the Software, unless such copies or derivative
works are solely in the form of machine-executable object code generated by
a source language processor.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
(70) Biopython
Biopython License Agreement
Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.
THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.
(71)
Copyright Notice for PHYLIP-New
The following copyright notice is intended to cover all source code, all
documentation, and all executable programs of the PHYLIP package.
� Copyright 1980-20089 University of Washington. All rights reserved.
Permission is granted to reproduce, perform, and modify these programs and
documentation files. Permission is granted to distribute or provide access to
these programs provided that this copyright notice is not removed, the programs
are not integrated with or called by any product or service that generates
revenue, and that your distribution of these documentation files and programs
are free. Any modified versions of these materials that are distributed or
accessible shall indicate that they are based on these programs. Institutions
of higher education are granted permission to distribute this material to their
students and staff for a fee to recover distribution costs. Permission requests
for any other distribution of these program should be directed to license (at)
u.washington.edu .
(72) Readseq 1.7
# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/Attic/vienna-rna-1.8.3.ebuild,v 1.3 2009/10/31 18:11:01 weaver Exp $
EAPI="2"
inherit toolchain-funcs multilib autotools perl-module
DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
LICENSE="vienna-rna"
HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86 ~ppc"
DEPEND="dev-lang/perl
media-libs/gd"
RDEPEND="${DEPEND}"
S="${WORKDIR}/ViennaRNA-${PV}"
PATCHES=(
"${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
"${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch
"${FILESDIR}"/${P}-gcc4.3.patch
"${FILESDIR}"/${P}-disable-gd.patch
)
src_prepare() {
base_src_prepare
sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
sed -i '1 i #include ' RNAforester/src/rnafuncs.cpp || die
eautoreconf
(cd RNAforester; eautoreconf)
}
src_configure() {
econf --with-cluster || die "Configuration failed."
sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
-i RNAforester/g2-0.70/Makefile \
|| die "Failed patching RNAForester build system."
sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
-i Readseq/Makefile || die "Failed patching readseq Makefile."
}
src_compile() {
emake clean || die
emake || die "Compilation failed."
emake -C Readseq || die "Failed to compile readseq."
# TODO: Add (optional?) support for the NCBI toolkit.
}
src_test() {
cd "${S}"/Perl && emake check || die "Perl tests failed"
cd "${S}"/Readseq && emake test || die "Readseq tests failed"
}
src_install() {
make install DESTDIR="${D}" || die "Installation failed."
dodoc AUTHORS ChangeLog NEWS README THANKS \
|| die "Failed to install documentation."
newbin Readseq/readseq readseq-vienna \
|| die "Installing readseq failed."
dodoc Readseq/Readseq.help || die \
"Readseq Documentation installation failed."
newdoc Readseq/Readme README.readseq && \
newdoc Readseq/Formats Formats.readseq \
|| die "Installing readseq Readme failed."
# remove perlocal.pod to avoid file collisions (see #240358)
fixlocalpod || die "Failed to remove perlocal.pod"
}
(73) Vienna RNA 1.8.25
The Vienna RNA package
See http://www.tbi.univie.ac.at/~ivo/RNA/
Disclaimer and Copyright
The programs, library and source code of the Vienna RNA Package are free
software. They are distributed in the hope that they will be useful
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Permission is granted for research, educational, and commercial use
and modification so long as 1) the package and any derived works are not
redistributed for any fee, other than media costs, 2) proper credit is
given to the authors and the Institute for Theoretical Chemistry of the
University of Vienna.
If you want to include this software in a commercial product, please contact
the authors.
Reference:
Ivo L Hofacker and Martin Fekete and Peter F Stadler
Secondary structure prediction for aligned RNA sequences.
J Mol Biol. 2002 vol. 319 (18) pp.3724-32
(74) Cdbfasta
Copyright for “cdbfasta” source package in Saucy
Ubuntu
Saucy (13.10)
“cdbfasta” source package
Copyright
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: cdbfasta
Upstream-Contact: Geo Pertea ,
Source: http://sourceforge.net/projects/cdbfasta/files/
Files: *
Copyright: © 2002-2010 Geo Pertea ,
Valentin Antonescu
The Institute for Genomic Research
License: PD
Date: Mon, 17 Dec 2012 11:26:54 -0500
From: Geo
To: andreas@an3as.eu
CC: valentin antonescu
Subject: Re: Fwd: Please forward to Geo Pertea: What exat license for cdbfasta?
.
Hi Andreas,
I don't think about the licensing issue much and this may be related to
the fact that the cdbfasta code if heavily based on Daniel J. Bernstein
's cdb source code
which has been notably license-free
. However, since DJB
released his individual source code files to public domain we also
consider the whole cdbfasta code to be public domain, free and open
source software.
.
Thanks,
--geo
Files: debian/*
Copyright: © 2010 Steffen Moeller
© 2012 Andreas Tille
License: GPL-3
On Debian systems, the full text of the GNU General Public License version 3
can be found in the file `/usr/share/common-licenses/GPL-3'.
(75) Jalview
Jalview is an Open Source project funded by the BBSRC.
The source is made available under the GNU General Public License (v3) as a gzipped tar file, which expands to a directory named jalview.
You will need J2SDK 1.6+ to build Jalview. All additional dependencies are provided in the source archive.
Full instructions for building the source are given in jalview/doc/building.html. To summarise, there are two ways to build Jalview :
Apache Ant
For the impatient: ant with no arguments will build the application, ant with the "makeApplet" target will build the applet.
Use a Java Integrated Development Environment.
Jalview 2 has been developed with two IDEs:
Eclipse
If you are new to eclipse, we recommend you install it with the Yoxos system.
Borland JBuilder
Jalview version 2 was originally developed using JBuilder, up until the release of version 2.3. There are two project files in the root directory of the archive, one for the application and another for the applet. Note: some dependencies will be missing from this project definition - check the ant build file.
Polite notice: If you want to change Jalview in a way that would benefit others in the community, please email us your code or suggestions and we will do our best to incorporate your ideas in future releases!
(76) Boxshade
DISTRIBUTION POLICY
---------------------------------------------------------------------------
BOXSHADE is completely public-domain and may be passed around and modified without any notice to the author. If you have problems, suggestions or remarks, please contact either of us:
Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848
MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany
E-mail: Kay.Hofmann@memorec.com
Michael D. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K.
E-mail: michael.baron@bbsrc.ac.uk
(77) Garlic
Copyright (c) 2008-2009 Ian White - ian.w.white@ardes.com
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
(78) Chemtool
FSF Licensing & Compliance Team
by Josh Gay — Published on Feb 10, 2005 04:06 PM
For over 20 years the FSF Licensing & Compliance Lab has been the preeminent resource of free licensing for free software developers.
Education & Support
We have a number of online resources as well as community-based and paid support.
See our licensing recommendations, analysis, and FAQ
Guide to choosing a license for your own work
Comprehensive FAQ about the GNU Licenses
List of other licenses and whether they are free, copyleft, or compatible with the GPL.
Learn why we must put an end to software patents:
Visit EndSoftPatents.org
Get Involved on the LibrePlanet.org End Software Patents Group
Join the action alert mailing list
Keep up to date with the latest licensing issues by visiting our License and Compliance blog, or subscribe to the Licensing and Compliance Blog RSS feed RSS feed
Have a question that you couldn't find the answer to? For general free software licensing questions please email licensing@fsf.org. Our team of licensing volunteers along with FSF staff will gladly answer questions for free software community members. We also offer paid support to proprietary software developers.
Copyright & Compliance
The Free Software Foundation holds the copyright to many GNU packages, such as GCC and EMACS. When hackers contribute to these projects, we ask that they assign their copyright to enable us to enforce the license. For questions about assigning to the FSF, please contact us at assign@gnu.org.
Free software is everywhere these days, inside our computers, phones, and even televisions. With so much free software being distributed every day, we have to remain vigilant against potential violations. You can help to make sure that free software is always free by reporting violations to our compliance lab.
The FSF can only enforce the license on works to which we hold the copyright, but we can still help bring about compliance even when the copyright lies elsewhere. If you need help with enforcement, please don't hesitate to contact us at license-violation@gnu.org
Verification & Certification
Fully free GNU/Linux Distributions. These distributions meet our guidelines for a fully free distro, and are fully committed to keeping their distributions free.
You can help keep those distributions free and earn a GNU Buck by filing a bug regarding a licensing issue in one of our endorsed distributions and sending an email to report-nonfree@fsf.org.
The Free Software Directory is our community curated listing of over 6500 free software packages. A great resource for finding and promoting software that respects its users.
Respects Your Freedom Hardware certification program
Looking to buy hardware that works well with free software? Check out h-node, a community run project to catalog how well different pieces of hardware work with fully free software.
(79) BallView
Announcement: BALL 1.1 released
We are happy to announce the release of BALL 1.1 and BALLView 1.1.
After significant modifications in the viewer, we are now releasing the next version of BALLView and BALL as release 1.1 (the differences are listed in our change log ). Here we list just the most essential changes:
BALL and BALLView are now licensed under the Lesser GNU Public License (LGPL) and the GNU Public License (GPL), respectively.
For the first time, we offer full support of BALLView as a native MacOS X application.
New models (ribbon mode, cartoon models for nucleic acids)
New coloring methods (by chain)
General overhaul of the BALLView dialogs
Some major bugfixes
As usual, you can download the latest version in the "downloads section"Downloads of this website.
Enjoy the new version and let us know what you think of it!
The BALL Team
(80) ConCavity
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: concavity
Upstream-Contact: Thomas Funkhouser
John A. Capra
Source: http://compbio.cs.princeton.edu/concavity/
Files: pkgs/R3Shapes/ply.*
Copyright: 1994 The Board of Trustees of The Leland Stanford Junior University.
All rights reserved.
License:
Permission to use, copy, modify and distribute this software and its
documentation for any purpose is hereby granted without fee, provided
that the above copyright notice and this permission notice appear in
all copies of this software and that you do not sell the software.
.
THE SOFTWARE IS PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND,
EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY
WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
Files: debian/*
Copyright: 2012 Laszlo Kajan
License: GPL-3.0+
Files: *
Copyright: 2009 John A. Capra and Thomas Funkhouser
License: GPL-3.0+
License: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
.
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
(81) DSSP
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.
Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.
You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.
c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.
In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.
3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.
5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License.
7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.
10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
one line to give the program's name and an idea of what it does.
Copyright (C) yyyy name of author
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details
type `show w'. This is free software, and you are welcome
to redistribute it under certain conditions; type `show c'
for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright
interest in the program `Gnomovision'
(which makes passes at compilers) written
by James Hacker.
signature of Ty Coon, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License.
(82) Cain
Copyright 2012 Alex Angelini
All rights reserved.
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.
(83) Python-rdkit
Terms and conditions for accessing or otherwise using Python
PSF LICENSE AGREEMENT FOR PYTHON 2.7.5
This LICENSE AGREEMENT is between the Python Software Foundation (“PSF”), and the Individual or Organization (“Licensee”) accessing and otherwise using Python 2.7.5 software in source or binary form and its associated documentation.
Subject to the terms and conditions of this License Agreement, PSF hereby grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use Python 2.7.5 alone or in any derivative version, provided, however, that PSF’s License Agreement and PSF’s notice of copyright, i.e., “Copyright © 2001-2013 Python Software Foundation; All Rights Reserved” are retained in Python 2.7.5 alone or in any derivative version prepared by Licensee.
In the event Licensee prepares a derivative work that is based on or incorporates Python 2.7.5 or any part thereof, and wants to make the derivative work available to others as provided herein, then Licensee hereby agrees to include in any such work a brief summary of the changes made to Python 2.7.5.
PSF is making Python 2.7.5 available to Licensee on an “AS IS” basis. PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 2.7.5 WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON 2.7.5 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 2.7.5, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
This License Agreement will automatically terminate upon a material breach of its terms and conditions.
Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between PSF and Licensee. This License Agreement does not grant permission to use PSF trademarks or trade name in a trademark sense to endorse or promote products or services of Licensee, or any third party.
By copying, installing or otherwise using Python 2.7.5, Licensee agrees to be bound by the terms and conditions of this License Agreement.
BEOPEN.COM LICENSE AGREEMENT FOR PYTHON 2.0
BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1
This LICENSE AGREEMENT is between BeOpen.com (“BeOpen”), having an office at 160 Saratoga Avenue, Santa Clara, CA 95051, and the Individual or Organization (“Licensee”) accessing and otherwise using this software in source or binary form and its associated documentation (“the Software”).
Subject to the terms and conditions of this BeOpen Python License Agreement, BeOpen hereby grants Licensee a non-exclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use the Software alone or in any derivative version, provided, however, that the BeOpen Python License is retained in the Software, alone or in any derivative version prepared by Licensee.
BeOpen is making the Software available to Licensee on an “AS IS” basis. BEOPEN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, BEOPEN MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
BEOPEN SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF THE SOFTWARE FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
This License Agreement will automatically terminate upon a material breach of its terms and conditions.
This License Agreement shall be governed by and interpreted in all respects by the law of the State of California, excluding conflict of law provisions. Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between BeOpen and Licensee. This License Agreement does not grant permission to use BeOpen trademarks or trade names in a trademark sense to endorse or promote products or services of Licensee, or any third party. As an exception, the “BeOpen Python” logos available at http://www.pythonlabs.com/logos.html may be used according to the permissions granted on that web page.
By copying, installing or otherwise using the software, Licensee agrees to be bound by the terms and conditions of this License Agreement.
CNRI LICENSE AGREEMENT FOR PYTHON 1.6.1
This LICENSE AGREEMENT is between the Corporation for National Research Initiatives, having an office at 1895 Preston White Drive, Reston, VA 20191 (“CNRI”), and the Individual or Organization (“Licensee”) accessing and otherwise using Python 1.6.1 software in source or binary form and its associated documentation.
Subject to the terms and conditions of this License Agreement, CNRI hereby grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use Python 1.6.1 alone or in any derivative version, provided, however, that CNRI’s License Agreement and CNRI’s notice of copyright, i.e., “Copyright © 1995-2001 Corporation for National Research Initiatives; All Rights Reserved” are retained in Python 1.6.1 alone or in any derivative version prepared by Licensee. Alternately, in lieu of CNRI’s License Agreement, Licensee may substitute the following text (omitting the quotes): “Python 1.6.1 is made available subject to the terms and conditions in CNRI’s License Agreement. This Agreement together with Python 1.6.1 may be located on the Internet using the following unique, persistent identifier (known as a handle): 1895.22/1013. This Agreement may also be obtained from a proxy server on the Internet using the following URL: http://hdl.handle.net/1895.22/1013.”
In the event Licensee prepares a derivative work that is based on or incorporates Python 1.6.1 or any part thereof, and wants to make the derivative work available to others as provided herein, then Licensee hereby agrees to include in any such work a brief summary of the changes made to Python 1.6.1.
CNRI is making Python 1.6.1 available to Licensee on an “AS IS” basis. CNRI MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, CNRI MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 1.6.1 WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON 1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
This License Agreement will automatically terminate upon a material breach of its terms and conditions.
This License Agreement shall be governed by the federal intellectual property law of the United States, including without limitation the federal copyright law, and, to the extent such U.S. federal law does not apply, by the law of the Commonwealth of Virginia, excluding Virginia’s conflict of law provisions. Notwithstanding the foregoing, with regard to derivative works based on Python 1.6.1 that incorporate non-separable material that was previously distributed under the GNU General Public License (GPL), the law of the Commonwealth of Virginia shall govern this License Agreement only as to issues arising under or with respect to Paragraphs 4, 5, and 7 of this License Agreement. Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between CNRI and Licensee. This License Agreement does not grant permission to use CNRI trademarks or trade name in a trademark sense to endorse or promote products or services of Licensee, or any third party.
By clicking on the “ACCEPT” button where indicated, or by copying, installing or otherwise using Python 1.6.1, Licensee agrees to be bound by the terms and conditions of this License Agreement.
ACCEPT
CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2
Copyright © 1991 - 1995, Stichting Mathematisch Centrum Amsterdam, The Netherlands. All rights reserved.
Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of Stichting Mathematisch Centrum or CWI not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission.
STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
Licenses and Acknowledgements for Incorporated Software
This section is an incomplete, but growing list of licenses and acknowledgements for third-party software incorporated in the Python distribution.
(84) Raccoon
Copyright for “raccoon” source package in Precise
Ubuntu
Precise (12.04)
“raccoon” source package
Copyright
Format: http://dep.debian.net/deps/dep5
Upstream-Name: raccoon
Source: http://autodock.scripps.edu/resources/raccoon
Files: *
Copyright: 2009 Stefano Forli
Molecular Graphics Lab
The Scripps Research Institute
License: GPL-3.0+
Files: debian/*
Copyright: 2011 Steffen Moeller
License: GPL-3.0+
License: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
.
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
(85) OpenClinica
About The GNU LGPL Open Source License
OpenClinica, copyright (C) 2005-2013 OpenClinica, LLC, is distributed under the GNU Lesser General Public License (GNU LGPL). OpenClinica is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
GNU emblemThe GNU Lesser General Public License (GNU LGPL) is summarized in the Creative Commons text below, and also available at http://creativecommons.org/licenses/LGPL/2.1/. The full, legal text of the license is available at http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html.
The GNU Lesser General Public License is a Free Software license. Like any Free Software license, it grants to you the four following freedoms:
The freedom to run the program for any purpose.
The freedom to study how the program works and adapt it to specific needs.
The freedom to redistribute copies so you can help your neighbor.
The freedom to improve the program and release your improvements to the public, so that the whole community benefits.
You may exercise the freedoms specified here provided that you comply with the express conditions of this license.
The principal conditions are:
You must conspicuously and appropriately publish on each copy distributed an appropriate copyright notice and disclaimer of warranty and keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of the GNU Lesser General Public License along with the Program. Any translation of the GNU Lesser General Public License must be accompanied by the GNU Lesser General Public License.
If you modify your copy or copies of the library or any portion of it, you may distribute the resulting library provided you do so under the GNU Lesser General Public License. However, programs that link to the library may be licensed under terms of your choice, so long as the library itself can be changed. Any translation of the GNU Lesser General Public License must be accompanied by the GNU Lesser General Public License.
If you copy or distribute the library, you must accompany it with the complete corresponding machine-readable source code or with a written offer, valid for at least three years, to furnish the complete corresponding machine-readable source code. You need not provide source code to programs which link to the library.
Any of these conditions can be waived if you get permission from the copyright holder.
Your fair use and other rights are in no way affected by the above.
For the full GNU LGPL License text, see LICENSE.txt included in the OpenClinica download package.
(86) Abinit
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy. The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.
A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
1. Source Code.
The "source code" for a work means the preferred form of the work
for making modifications to it. "Object code" means any non-source
form of a work.
A "Standard Interface" means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that
is widely used among developers working in that language.
The "System Libraries" of an executable work include anything, other
than the work as a whole, that (a) is included in the normal form of
packaging a Major Component, but which is not part of that Major
Component, and (b) serves only to enable use of the work with that
Major Component, or to implement a Standard Interface for which an
implementation is available to the public in source code form. A
"Major Component", in this context, means a major essential component
(kernel, window system, and so on) of the specific operating system
(if any) on which the executable work runs, or a compiler used to
produce the work, or an object code interpreter used to run it.
The "Corresponding Source" for a work in object code form means all
the source code needed to generate, install, and (for an executable
work) run the object code and to modify the work, including scripts to
control those activities. However, it does not include the work's
System Libraries, or general-purpose tools or generally available free
programs which are used unmodified in performing those activities but
which are not part of the work. For example, Corresponding Source
includes interface definition files associated with source files for
the work, and the source code for shared libraries and dynamically
linked subprograms that the work is specifically designed to require,
such as by intimate data communication or control flow between those
subprograms and other parts of the work.
The Corresponding Source need not include anything that users
can regenerate automatically from other parts of the Corresponding
Source.
The Corresponding Source for a work in source code form is that
same work.
2. Basic Permissions.
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However, if you cease all violation of this License, then your
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holder fails to notify you of the violation by some reasonable means
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Moreover, your license from a particular copyright holder is
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received notice of violation of this License (for any work) from that
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your receipt of the notice.
Termination of your rights under this section does not terminate the
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reinstated, you do not qualify to receive new licenses for the same
material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
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10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
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You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
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rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
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sale, or importing the Program or any portion of it.
11. Patents.
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License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
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but do not include claims that would be infringed only as a
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available, or (2) arrange to deprive yourself of the benefit of the
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consistent with the requirements of this License, to extend the patent
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actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
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arrangement, you convey, or propagate by procuring conveyance of, a
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work and works based on it.
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the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
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or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
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12. No Surrender of Others' Freedom.
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to collect a royalty for further conveying from those to whom you convey
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License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
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License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
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address new problems or concerns.
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option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
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by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
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to choose that version for the Program.
Later license versions may give you additional or different
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author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
(87) Openmax
OpenMaX is a graphic platform for Computational Electromagnetics and Computational
Optics on personal computers under Windows 95/98/ME/NT/2000/XP/Vista. We are working
on a Linux version.Copyright 2009, 2009 Christian Hafner, COG, IFH, ETH Zurich,
Switzerland
OpenMaX is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
(88) Ccwatcher
License
As only free software is good software, ccwatcher is placed under the GPL. That means you can download,
use, modify and redistribute it for free, amongst other freedoms. Licensing of material other than code
(icons etc.) can be found in the license.txt file of the package, but be assured everything follows an
open-content philosophy.
(89) Kalzium
Copyright for “kalzium” source package in Precise
Ubuntu
Precise (12.04)
“kalzium” source package
Copyright
Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?view=markup&pathrev=174
Comment: This package was developed for Ubuntu by the Kubuntu Developers and
modified to be included in Debian. See below the copyright holders for debian/*
files.
Files: *
Copyright: 2003-2008 by Carsten Niehaus
2007-2008 by Marcus D. Hanwell
2005 by Inge Wallin
2005, 2006 by Pino Toscano, toscano.pino@tiscali.it
2009-2010 by Etienne Rebetez, etienne.rebetez@oberwallis.ch
2009 by Kashyap R Puranik
2006, 2007 by Jerome Pansanel
2006 by Georges Khaznadar
2007 by Johannes Simon
2004 by Thomas Nagy
License: GPL-2+
Files: debian/*
Copyright: 2011 Kubuntu Developers
Copyright: 2011 Debian Qt/KDE Maintainers
License: GPL-2+
Files: src/unitsettingsdialog.* src/kalziumunitcombobox.*
Copyright: 2011 Rebetez Etienne
License: GPL-3+
Files: compoundviewer/libkdeedu_compoundviewer_export.h libscience/libkdeedu_science_export.h
Copyright: 2007 David Faure
License: LGPL-2+
Files: doc/*
Copyright: 2001, 2002, 2004, 2005, 2006, 2007, 2008 Carsten Niehaus
2005 Anne-Marie Mahfouf
License: GFDL-1.2
Files: cmake/modules/*
Copyright: 2006, 2007 Montel Laurent,
2008, 2009 Gael Guennebaud,
2006, 2007, Carsten Niehaus,
2006, 2007, 2009, Pino Toscano,
2008, Albert Astals Cid,
2008 Marcus D. Hanwell
License: BSD-3-clause
Files: src/psetable/*
Copyright: 2007-2009 by Marcus D. Hanwell
2010-2011 by Etienne Rebetez
2005-2006 by Pino Toscano, toscano.pino@tiscali.it
2003-2006 by Carsten Niehaus, cniehaus@kde.org
License: LGPL-2.1
Files: src/psetable/statemachine.h
Copyright: 2010 Nokia Corporation and/or its subsidiary(-ies).
License: BSD-3-clause
License: GPL-2+
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
.
On Debian systems, the full text of the GNU General Public License
version 2 can be found in the file
`/usr/share/common-licenses/GPL-2'.
License: GPL-3+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
.
On Debian systems, the full text of the GNU General Public License
version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
License: GFDL-1.2
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.2
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the section entitled "GNU
Free Documentation License".
.
On Debian systems, the full text of the GNU Free Documentation
License version 1.2 can be found in the file
`/usr/share/common-licenses/GFDL-1.2'.
License: LGPL-2+
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Library General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Library General Public License for more details.
.
You should have received a copy of the GNU Library General Public License
along with this library; see the file COPYING.LIB. If not, write to
the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
Boston, MA 02110-1301, USA.
.
On Debian systems, the full text of the GNU Lesser General Public
License version 2 can be found in the file
`/usr/share/common-licenses/LGPL-2'.
License: LGPL-2.1
This file is part of the Avogadro molecular editor project.
For more information, see
.
Kalzium is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation; either version 2.1 of the License, or
(at your option) any later version.
.
Avogadro is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301, USA.
.
On Debian systems, the full text of the GNU Lesser General Public
License version 2.1 can be found in the file
`/usr/share/common-licenses/LGPL-2.1'.
License: BSD-3-clause
"Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution.
* Neither the name of Nokia Corporation and its Subsidiary(-ies) nor
the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
$QT_END_LICENSE$
(90) Gabedit
Copyright for “gabedit” source package in Lucid
Ubuntu
Lucid (10.04)
“gabedit” source package
Copyright
This package was debianized by Daniel Leidert (dale)
on Thu, 2 Sep 2004 23:12:54 +0200.
It was downloaded from:
http://downloads.sourceforge.net/gabedit/
Copyright:
2002-2007 Abdul-Rahman Allouche
Upstream Author:
Abdul-Rahman Allouche
License:
All rights reserved
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the Gabedit), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
IN THE SOFTWARE.
==============================================================================
The shipped of GtkGLArea contains the following Copyright and license:
Copyright (C) 1997-1998 Janne Löf
Copyright (C) 2000 Marc Flerackers
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Library General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
On Debian systems, a copy of the GNU Lesser General Public License (LGPL) can
be found at /usr/share/common-licenses/LGPL.
==============================================================================
The files utils/Others/elements.txt and utils/Others/myElements.txt have been
taken from the openbabel package and are shipped under the following license:
Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (c) 2001-2003 Geoffrey R. Hutchison
Part of the Open Babel package, under the GNU General Public License (GPL)
On Debian systems, a copy of the GNU General Public License (GPL) can be found
at /usr/share/common-licenses/GPL.
(91) GChemCalc
hapter 4. License
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
A copy of the GNU General Public License is included as an appendix to the GNOME Users Guide. You may also obtain a copy of the GNU General Public License from the Free Software Foundation by visiting their Web site or by writing to
Free Software Foundation, Inc.
51 Franklin St - Fifth Floor
Boston, MA 02111-1307
USA
(92) Molrender
License
molrender is open-source software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
(93) Mopac7
Academics
MOPAC2012™ executables are available FREE for academic, not-for-profit use.
To request a license key and download, click here
If you have a license key already, download the latest version here
______________________________________________________________
Commercial and Government
For commercial and government sales, please contact CAChe Research
Pricing Information (Pricelist)
For current version number click here
For source code, see the Developers page
For consulting, contact CAChe Research
(94) Mpqc
MPQC is open-source software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
(95) Viewmol
# Copyright 1999-2012 Gentoo Foundation
2 # Distributed under the terms of the GNU General Public License v2
3 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/viewmol/viewmol-2.4.1-r2.ebuild,v 1.3 2012/10/06 16:25:53 jlec Exp $
4
5 EAPI=3
6
7 PYTHON_DEPEND="2"
8 PYTHON_USE_WITH="tk"
9
10 inherit eutils multilib prefix python toolchain-funcs
11
12 DESCRIPTION="Open-source graphical front end for computational chemistry programs"
13 HOMEPAGE="http://viewmol.sourceforge.net/"
14 SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz"
15
16 LICENSE="GPL-2"
17 SLOT="0"
18 KEYWORDS="~amd64 ~x86"
19 IUSE=""
20
21 RDEPEND="
22 media-libs/libpng
23 media-libs/tiff
24 virtual/glu
25 virtual/opengl
26 x11-libs/libX11
27 x11-libs/libXi
28 x11-libs/libXmu
29 x11-libs/libXt
30 >=x11-libs/motif-2.3:0"
31 DEPEND="${RDEPEND}
32 x11-proto/inputproto
33 x11-proto/xproto"
34
35 S="${WORKDIR}/${P}/source"
36
37 pkg_setup() {
38 python_set_active_version 2
39 }
40
41 src_prepare() {
42 epatch \
43 "${FILESDIR}"/${PV}-remove-icc-check.patch \
44 "${FILESDIR}"/${PV}-change-default-paths.patch
45
46 eprefixify getrc.c
47 sed "s:GENTOOLIBDIR:$(get_libdir):g" \
48 -i install getrc.c || die
49 sed "s:GENTOODOCDIR:${PF}:g" -i install || die
50
51 LINKFORSHARED=$($(PYTHON) -c "import distutils.sysconfig; print distutils.sysconfig.get_config_var('LINKFORSHARED')")
52
53 mkdir $(uname -s) && cd $(uname -s)
54
55 cat >> .config.$(uname -s) <<- EOF
56 LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)"
57 TIFFINCLUDE = "${EPREFIX}/usr/include"
58 LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)"
59 PNGINCLUDE = "${EPREFIX}/usr/include"
60 PYTHONVERSION = $(PYTHON)
61 PYTHONINCLUDE = "${EPREFIX}/$(python_get_includedir)"
62 PYTHONLIB = "${EPREFIX}/usr/$(get_libdir)"
63 COMPILER = $(tc-getCC)
64 CFLAGS = ${CFLAGS} -DLINUX
65 LDFLAGS = ${LDFLAGS} ${LINKFORSHARED}
66 SCANDIR=
67 INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) -I\$(PYTHONINCLUDE)
68 LIBRARY=\$(LIBTIFF) \$(LIBPNG) -L\$(LIBPYTHON)
69 LIBS=-L"${EPREFIX}/usr/$(get_libdir)" $(python_get_library -l) -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm
70 EOF
71
72 cp .config.$(uname -s) makefile
73 cat ../Makefile >> makefile
74 }
75
76 src_compile() {
77 pushd $(uname -s)
78 emake viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_ || die
79 popd
80 "${EPREFIX}"/bin/bash makeTranslations || die
81 }
82
83 src_install() {
84 ./install "${ED}"/usr || die
85 mv "${ED}"/usr/{usr/share,} || die
86 rm -rf "${ED}"/usr/usr
87 }
(95) Xdrawchem
Copyright for “xdrawchem” source package in Saucy
Ubuntu
Saucy (13.10)
“xdrawchem” source package
Copyright
Format: http://dep.debian.net/deps/dep5
Upstream-Name: xdrawchem
Source: svn export https://xdrawchem.svn.sourceforge.net/svnroot/xdrawchem/trunk/xdrawchem-qt4
Files: *
Copyright: 2001-2005 Bryan Herger
2001 Christoph Steinbeck (contributions)
License: GPL version 2+
see `/usr/share/common-licenses/GPL-2'.
Files: xdrawchem/sdg.h xdrawchem/setofrings.h xdrawchem/ring.h
Copyright: 1997-2000 The JChemPaint project
License: GNU Lesser General Public License 2.1 as published by the
Free Software Foundation; either version 2.1 of the License, or
(at your option) any later version.
.
see `/usr/share/common-licenses/LGPL-2.1'
Files: xdrawchem/boshcp.h xdrawchem/application.cpp xdrawchem/CMakeFiles/xdrawchem.dir/application.cpp.o xdrawchem/sorf.h xdrawchem/boshcp.cpp xdrawchem/molecule_smiles.cpp
Copyright: 1997 - 2000 Dr. Christoph Steinbeck
License: artistic license
This software is published and distributed under artistic license.
The intent of this license is to state the conditions under which this Package
may be copied, such that the Copyright Holder maintains some semblance
of artistic control over the development of the package, while giving the
users of the package the right to use and distribute the Package in a
more-or-less customary fashion, plus the right to make reasonable modifications.
.
THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND
FITNESS FOR A PARTICULAR PURPOSE.
.
The complete text of the license can be found in a file called LICENSE
accompanying this package.
Files: debian/*
Copyright: 2011 Georges Khaznadar
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".