Question 9: If I use the package codes to develop new codes with different applications, would it be a copyright violation?

Question 10: How do I decide which of the three variants of a software in OSDDLinux to use - standalone, webserver or galaxy?

Question 11: Which flavors of linux support OSDDLinux and which of these is recommended for best performance?


Question 12: What all biological or chemical research problems are being addressed by the tools in OSDDLinux?

Question 13: How many of the bioinformatics or cheminformatics tools included in OSDDLinux have been published in international journals?

Question 14: How much does it cost for using OSDDLinux?

Question 15: In what all flavors of linux is OSDDLinux available?

Question 16: Is it better to use bioinformatics and cheminformatics tools from OSDDLinux than using the same tools from webservers available online? If yes, how?

Question 17: Does OSDDLinux also include bioinformatics freeware not developed by OSDD?

Question 18: Does OSDDLinux provide example usage of the informatics sotware?

Answer 1: It is a linux-based customize operating system for drug discovery

Answer 1: Council of Scientific and Industrial Research (CSIR) support OSDD-Linux under project OSDD and GENESIS.

Answer 1: Main objective of OSDD-Linux is to promote OSDD in order to provide afforable drugs for poors.

Answer 1: It provides in silico plateform for discovering drugs which may play vital role in reducing cost and time on discovering a drug molecule.

Answer 1: Custimize linux developed in past (like Biolinux, DNALinux, BioSlax, VigyanCD) only focus on bioinformatics. Drug informatics comprises number of informatics like Chemoinformatics, Pharmainformatics, immunoinformatics, Bioinformatics. Best of our know OSDD-Linux is first attempt which cover most of informatics important for drug discovery.

Answer 1: Yes one can use all modules of OSDD-linux online via Internet from OSDD-Linux Live Server.

Answer 1: Due to limitation computational resources, most of our CPU-intensive computer server will allow to process limitted sequences/molecules. Security of your molecules and limitation large data transfer is other limitations.

Answer 2: Any local machine based on unix operating system with around 50 MB of space available for dedication can support OSDD-Linux. For windows and mac users, a virtual ware like the freely available VirtualBox (available at https://www.virtualbox.org/wiki/Downloads) or any commercial virtual desktop is required to launch OSDD-Linux concurrently with the running windows or mac OS.

Answer 3: The current version of OSDD-Linux is not available for installation on windows or mac operating systems. However, virtual desktops like VirtualBox can be used to launch OSDD-Linux on these systems.

Answer 4: OSDD-Linux can be made to run on a mac system using the virtual desktops like VMware or Virtual Box.

Answer 5: OSDD-Linux is available for download and/or installation as an ISO image file. The user can either boot the live CD from which the OSDD-Linux could be directly used or the user can install OSDD-Linux on hard disk using the Install option. In case of virtual ware, the ubuntu would directly launch OSDD-Linux in virtual desktop. If OSDD-Linux is required to run on an ubuntu desktop, the iso image file essentilly needs to be burnt on a CD/DVD.

Answer 6: 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. OSDD-Linux on the other hand has been designed to cater the demands of research community in the field of bioinformatics and cheminformatics. Accordingly, the tools provided in OSDD-Linux 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 OSDD-Linux that would otherwise require installation on a standard Linux version.

Answer 7: Yes, the current release of OSDD-Linux has been built on the standard Ubuntu version and the home folder has been changed along with changes in the PATH variable.

Answer 8: The source code of OSDD-Linux has been made available at http://crdd.osdd.net/osddlinux/sources.php

Answer 9: All the tools provided by OSDD-Linux 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 OSDD-Linux programs for developing new programs in OSDD-Linux is not a copyright violation.

Answer 10: Choice of the software variant depends on the size of the data to be analyzed as well as the convinience 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, OSDD-Linux attempts to extend the bioinformatics and cheminformatics facilities to every potential user.

Answer 11: At present OSDD-Linux is available only in Ubuntu 12.04.

Answer 12: In cheminformatics, the tools provided by OSDD-Linux serve a wide diversity of chemical or drug research practices from basic visualization (Jmol, Pymol) and format conversion (BABEL) to advance operations like docking (Autodock), compound screening (PyRx) and scaffold hunting (ScaffoldHunter). Bioinformatics tools include basic sequence analisys 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 OSDD-Linux 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 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 an 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.

Answer 13: All the softwares in OSDD-Linux that have been developed in-house are published in peer-reviewed journals.

Answer 14: OSDD-Linux is available absolutely free and is licensed under GNU-General Public License.

Answer 15: At present, OSDD-Linux is available only in Ubuntu 12.04.

Answer 16: Webservices made available for bioinformatics and cheminformatics gives 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 cheminformatics 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.

Answer 17: Yes, OSDDLinux includes a lot of popular and routinely used bioinformatics and cheminformatics tools like cd-hit, blast, clustalw, phylip, babel, pymol, rasmol, modeller, etc. apart from the softwares developed by OSDD.

Answer 18: For each of the software tools developed by OSDD that run 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.

Answer 19: The recommended memory allocation for running OSDD-Linux on VirtualBox is around 50 MB.

Answer 20: The galaxy version of 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.

Answer 21: All the dependencies of the software in OSDD-Linux have been included within the /gpsr/software/ directory in the package. So the issues of dependencies has already been taken care of.

Answer 22: The current version of OSDD-Linux is built on Ubuntu 12.04.

Answer 23: 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 OSDD-Linux user.

Answer 24: For the users facing deficiency of infrastructure both hardware and software, the web portal of OSDD-Linux provides link to the "LIVE SERVER". The Live Server allows the user to use OSDD-Linux on the host server of OSDD-Linux. 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.

Answer 25: The details for the installation are available at http://crdd.osdd.net/osddlinux/livecd.php

Answer 26: The current version of OSDD-linux has not been customized for usage over a network but work is in progress to do so.

Answer 27: The executables for the dependency should be put in the directory /gpsr/software/ and if the dependency uses a database the same shoul be placed in the directory /gpsr/data/

Answer 28: When OSDD-Linux is installed on the local machine or is used from live CD/DVD or USB without installation, the user is logged in as the root.

Answer 29: ..

Answer 30: OSDD-Linux provides the basic architecture and platform for launching webservices using a freely available open source software Apache linked with PHP. Some of the webservicces from Dr. Raghava's group are already working in OSDD-Linux. 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.

Answer 31: The current release of OSDD-Linux runs on 64 bit machines.

Answer 32: The user can find a list of perl scripts used to develop softwares by OSDD in-house softwares in OSDD-Linux at http://crdd.osdd.net/osddlinux/gpackage.php

Answer 33: OSDD-Linux is updated every six months.

Answer 34: The conducive usage of OSDD-Linux 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 OSDD-Linux on this virtual desktop.

Answer 34: Built on a standard and popular linux flavor (ubuntu), OSDD-Linux 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.

Answer 34: You can contribute to the development of OSDD-Linux in several ways-
(a) The users may send feedback suggestions directly to the OSDD as these are valuable for the continuous improvement of the OSDD-Linux to serve the demands of the users.
(b) The user may download and host a mirror site for OSDD-Linux. This would help in free distribution of OSDD-Linux.
(c) The user may maintain a mirror site of the LIVE SERVER of OSDD-Linux 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 webserversrelated to drug discovery and send it to the OSDD team. The developed tool may be included in the subsequent release of OSDD-Linux.

Answer 34: Besides including the popular open sourcce softwares in bioinformatics and cheminformatics, OSDD-Linux 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 OSDD-Linux. Thus, OSDD-Linux 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 cheminformatics developed in-house.