Question 1. What is OSDDlinux?

It is a linux-based customized operating system for drug discovery.

Question 2. Who supports OSDDlinux?

Council of Scientific and Industrial Research (CSIR) supports OSDDlinux under project OSDD and GENESIS.

Question 3. What is the purpose of OSDDlinux?

Main objective of OSDDlinux is to promote OSDD in order to provide afforable drugs for poors.

Question 4. How OSDDlinux can play role in discovering affordable drugs?

It provides in silico platform for discovering drugs which may play vital role in reducing cost and time on discovering a drug molecule. It is free, so any one can use this platform/infrastructure for drug disovery. This may also promote crowdsourcing for drug development.

Question 5. Why another Linux (Linux for bioinformatics already available)?

Customized linux developed in past (like Biolinux, DNALinux, BioSlax, VigyanCD) only focus on bioinformatics. Drug informatics comprises number of informatics like Chemoinformatics, Pharmacoinformatics, Immunoinformatics, Bioinformatics. To the best of our knowledge, OSDDlinux is first attempt which covers most of informatics important for drug discovery.

Question 6. Can I use OSDDlinux without installing it on my computer?

Yes, one can use all modules of OSDDlinux online via Internet from OSDDlinux Live Server.

Question 7. What is limitation of OSDDlinux Live Server?

Due to limitations of computational resources, most of our CPU-intensive computer server will allow to process limited sequences/molecules. Security of your molecules and limitations of large data transfer are other limitations.

Question 8. What is minimum requirement for OSDDlinux?

Any machine based on linux operating system with around 512 MB RAM and 10 GB of space on hardisk can support OSDDlinux. For windows and mac users, VirtualBox (available at https://www.virtualbox.org/wiki/Downloads) or any commercial virtual desktop is required to launch OSDDlinux.

Question 9. Can I install on Windows OS?

The current version of OSDDlinux is not available for installation on windows or mac operating systems. However, virtual desktops like VirtualBox can be used to launch OSDDlinux on these systems.

Question 10. Can I run OSDDlinux on Mac?

OSDDlinux can be made to run on a mac system using the virtual desktops like VMware or Virtual Box.

Question 11. Can I install on Windows OS?

OSDDlinux is available for download and/or installation as an ISO image file. The user can either boot the live CD from which the OSDDlinux could be directly used or the user can install OSDDlinux on hard disk using the Install option. In case of virtual ware, the ubuntu would directly launch OSDDlinux in virtual desktop. If OSDDlinux is required to run on an ubuntu desktop, the iso image file essentially needs to be burnt on a CD/DVD.

Question 12. What is different between Linux and OSDDlinux?

The standard version of a Linux flavor provided by the Linux community addresses the needs of a general user generating, storing and analyzing data that could arise from any academic or commercial field. Hence, Linux would hold the tools to manipulate and scrutinize text or numbers in general without any subject theories or principles in their algorithms. OSDDlinux on the other hand has been designed to cater the demands of research community in the field of bioinformatics and chemoinformatics. Accordingly, the tools provided in OSDDlinux are based on the well established physical, biological, chemical dogmas as well as mathematical and statistical machine learning techniques. These tools run as default commands with options on the terminal of OSDDlinux that would otherwise require installation on a standard Linux version.

Question 13. Is this modified version of Ubuntu?

Yes, the current release of OSDDlinux has been built on the standard Ubuntu version and the home folder has been changed along with changes in the PATH variable.

Question 14. How can I get source code of OSDDlinux?

The source code of OSDDlinux has been made available at http://osddlinux.osdd.net/prepo.php

Question 15. If I use the package codes to develop new codes with different applications, would it be a copyright violation?

All the tools provided by OSDDlinux have been developed under the GNU General Public License (GNU-GPL). This guarantees freedom to the user to share and change all versions of a program. Therefore, using OSDDlinux programs for developing new programs in OSDDlinux is not a copyright violation.

Question 16. How do I decide which of the three variants of a software in OSDDlinux to use - Standalone, Webserver or Galaxy?

Choice of the software variant depends on the size of the data to be analyzed as well as the convenience of the user in terms of familiarity with unix command line. If the data is less, the webservers can be locally launched and the data can be given as input to get the result in standard format. If the data is large, unix-savvy users would find running the standalones on the terminal much faster to have result files that could be further analyzed easily. On the other hand, Galaxy versions provide facitlity of analyzing bulk data to the users not comfortable with or having aversion to command line usage. Thus, OSDDlinux attempts to extend the bioinformatics and chemoinformatics facilities to every potential user.

Question 17. Which flavors of linux support OSDDlinux and which of these is recommended for best performance?


At present OSDDlinux is available only in Ubuntu 12.04.

Question 18. What all biological or chemical research problems are being addressed by the tools in OSDDlinux?

In chemoinformatics, the tools provided by OSDDlinux serve a wide diversity of chemicals or drug research practices from basic visualization (Jmol, Pymol) and format conversion (BABEL) to advanced operations like docking (Autodock), compound screening (PyRx) and scaffold hunting (ScaffoldHunter). Bioinformatics tools include basic sequence analysis tools like dalign, cd-hit, clustalw, phylip, etc. and next generation sequencing tools like samtools, bowtie, cufflinks, etc. as well as molecular dynamics simulation package (GROMACS). The "tour de force" facet of OSDDlinux is constituted by softwares developed by OSDD itself in four major categories viz. Vaccine Informatics, Drug targets, Biotherapeutics and Analysis of NGS data. The Vaccine informatics softwares include Epitope prediction tools (CTLPred, ABCPred, CBTope, LBTope) and MHC binding predictors (PROPRED1, nHLAPred). The Drug target module provides software like GPCRPred, ATPint, GTPbinder, etc. that predict whether a molecule would bind to GPCRs, ATP or GTP respectively to estimate their ability to work as drugs. In the module of Biotherapeutics, in-house softwares have been provided that include CellPPD for designing cell penetrating peptides, ToxinPred for predicting and designing toxic and non-toxic peptides, AntiBP for predicting antibacterial peptides in known protein sequences, etc. The section "Analysis of NGS data" hosts state-of-the-art automated pipeline for genome assembly and annotation of microbial genomes along with a server for benchmarking genome assemblers and a method for variation detection in paired normal/cancerous tissue data.

Question 19. How many bioinformatics or chemoinformatics tools have been included in OSDDlinux have been published in international journals?

All the softwares in OSDDlinux that have been developed in-house are published in peer-reviewed journals.

Question 20. How much does it cost for using OSDDlinux?

OSDDlinux is available absolutely free and is licensed under GNU-General Public License.

Question 21. In what all flavors of linux OSDDlinux is available?

At present, OSDDlinux is available only in Ubuntu 12.04.

Question 22. Is it better to use bioinformatics and chemoinformatics tools from OSDDlinux than using the same tools from webservers available online? If yes, how?

Webservices made available for bioinformatics and chemoinformatics give the advantage of access to the tool from anywhere using the internet services. Yet these services are limited by the internet speed and the size of data that webservers can handle. This is where a version of the tool that could be installed on the local machine becomes handy. On a local machine, the user can decide how much memory to dedicate to the running bioinformatics or chemoinformatics tools. This also pulls off the limit on the size of data which the tool can handle. Therefore, when available, OSDDlinux scores over webservers in terms of convenience of usage.

Question 23. Does OSDDlinux also include bioinformatics freeware not developed by OSDD?

Yes, OSDDlinux includes a lot of popular and routinely used bioinformatics and chemoinformatics tools like cd-hit, blast, clustalw, phylip, babel, pymol, rasmol, modeller, etc. apart from the softwares developed by OSDD.

Question 24. Does OSDDlinux provide example usage of the informatics sotware?

For each of the software tools developed by OSDD that runs as commands on command line terminal, if the user types only the name of the tool and presses enter, the usage is displayed on the terminal. After this, if the user executes the usage example (achieved from previous step) printed on the terminal, the program takes sample input file from /gpsr/examples/ directory, executes and provides the result output file of the sample input. This way the standalone versions of the softwares developed by OSDD explain the usage to the users.

Question 25. For using OSDDlinux on virtual machine, how much memory allocation is required by the virtual ware?

The recommended memory allocation for running OSDDlinux on VirtualBox is around 50 MB.

Question 26. What is the purpose of separately providing the galaxy version and the webserver variant of a software if both of them take input and provide output through graphical interface?

The galaxy version is capable of handling large size of data while the webserver is limited in its capacity to analyze the input and provide the results. Accordingly, both versions are provided to fulfil both conditions.

Question 27. Do I need to separately install the dependencies of the softwares in OSDDlinux?

All the dependencies of the software in OSDDlinux have been included within the /gpsr/software/ directory in the package. So the issues of dependencies has already been taken care of.

Question 28. Which version of Ubuntu would support OSDDlinux?

The current version of OSDDlinux is built on Ubuntu 12.04.

Question 29. I wish to add my own software to OSDDlinux, where (which directory) should I put the dependencies to give the paths to my software to make it operational in OSDDlinux?

The dependency softwares should be put in the directory /gpsr/software and accordingly the paths given to use them in a software developed and added by the OSDDlinux user.

Question 30. How does OSDDlinux support the users having issues of scarcity of resources like memory, new softwares, etc.?

For the users facing deficiency of infrastructure both hardware and software, the web portal of OSDDlinux provides link to the "LIVE SERVER". The Live Server allows the user to use OSDDlinux on the host server of OSDDlinux. At present, only the webserver and galaxy versions of softwares can be used on Live Server but the facility of using standalone through user login is also under consideration.

Question 31. Where can I get the step by step procedure for installation of OSDDlinux on my local machine?

The details for the installation are available at http://osddlinux.osdd.net/livecd.php

Question 32. Can I install and share OSDDlinux on a local network to facilitate multiple users within my institute/organization/group?

The current version of OSDDlinux has not been customized for usage over a network but work is in progress to do so.

Question 33. How should I install a new dependency for the new software I have developed individually within OSDDlinux?

The executables for the dependency should be put in the directory /gpsr/software/ and if the dependency uses a database the same should be placed in the directory /gpsr/data/

Question 34. Being a user am I logged in as the root when I boot OSDDlinux?

When OSDDlinux is installed on the local machine or is used from live DVD or USB without installation, the user is logged in as the root.

Question 35. Can I mount new tools in OSDDlinux from USB?

..

Question 36. Can I host my own webservices using OSDDlinux?

OSDDlinux provides the basic architecture and platform for launching webservices using a freely available open source software Apache linked with PHP. Some of the webservices from Dr. Raghava's group are already working in OSDDlinux. The user can host his/her own webservice from the /gpsr/webservers/cgidocs/ directory which is the root directory defined in the Apache configuration file.

Question 37. OSDDlinux runs on 32 bit system or 64 bit?

The current release of OSDDlinux runs on 64 bit machines.

Question 38. Where can I get a list of all the PERL scripts that come with OSDDlinux?

The user can find a list of PERL scripts used to develop softwares by OSDD in-house softwares in OSDDlinux at http://osddlinux.osdd.net/bscripts.php

Question 39. When is the next version of OSDDlinux coming out?

OSDDlinux is updated every six months.

Question 40. How can I use OSDDlinux on windows/linux/mac operating systems?

The conducive usage of OSDDlinux on windows and mac as well as linux flavors other than ubuntu is viable with the virtualware like VirtualBox. The user would first require to install Oracle VM Virtual Box available for download at https://www.virtualbox.org/wiki/Downloads and subsequently install OSDDlinux on this virtual desktop.

Question 41. How does OSDDlinux score advantage or disadvantage over standard Linux?

Built on a standard and popular linux flavor (ubuntu), OSDDlinux encompasses all types of drug discovery related libraries and packages available as freeware. Such a garner dedicated to drug discovery is not available in a standard linux system.

Question 42. How can I contribute to OSDDlinux if I wish to do so?

You can contribute to the development of OSDDlinux in several ways-
(a) The users may send feedback suggestions directly to the OSDD as these are valuable for the continuous improvement of the OSDDlinux to serve the demands of the users.
(b) The user may download and host a mirror site for OSDDlinux. This would help in free distribution of OSDDlinux.
(c) The user may maintain a mirror site of the LIVE SERVER of OSDDlinux on his/her website. The Live Server allows the user to avail and use the galaxy and webserver variants of softwares on the host server itself.
(d) In terms of developing new softwares, the user may develop his/her own softwares and webservers related to drug discovery and send it to the OSDD team. The developed tool may be included in the subsequent release of OSDDlinux.

Question 43. Does OSDDlinux include any new software also?

Besides including the popular open sourcce softwares in bioinformatics and chemoinformatics, OSDDlinux is the first to include the softwares devloped and provided as webservices by Dr. Raghava's Group. These softwares have been converted into three variants namely the standalone version, the galaxy version and the webserver set up, all three being included in OSDDlinux. Thus, OSDDlinux includes more than a HUNDRED new softwares/workflows available from Dr. Raghava's group. This is in strong contrast to similar efforts in the past like Biolinux and DNAlinux that did not include the freeware in bioinformatics and chemoinformatics developed in-house.