BIOINFORMATICS FACILITIES WITH C-DAC

(This blog post sums up details given at official site of Bioinformatics, C-DAC http://bioinfo-portal.cdac.in/. For more details, latest updates and verifications, please refer to the official portal. This is just to share the world class facilities available with the organization for researchers in different areas of Bio-Technology.)

Centre for Development of Advanced Computing (C-DAC) is the premier R&D organization of the Department of Electronics and Information Technology (DeitY), Ministry of Communications & Information Technology (MCIT), Government of India for carrying out R&D in IT, Electronics and associated areas.

A.   BIOINFORMATICS RESOURCES & APPLICATIONS FACILITY (BRAF) by C-DAC

 

              I.        INFORMATION ON BRAF

 

This blog post refers to the details given at - http://bioinfo-portal.cdac.in/braf.html

  

            II.        BRAF COMPUTING RESOURCES

·         BIOGENE - supercomputing environment

 

·         BIOCHROME - advance blade server based HPC facility

 

·         BIOBANK - data Storage solution

 

·         NGS Server - high memory CISCO UCS 450 server having 512 GB RAM and 32 computing cores

 

·         Hardware Acceleration using RCS Card

 

           III.        APPLICATION SOFTWARES ON BRAF

·         Sequence Analysis: FastA,BLAST, ClustalW, MEME, Phylip, AlignACE, cross match, EMBOSS, RAxML, Elph, Weeder , Primer3 , Seqclean , SIGNALP , Prophage, Mutual information

·         Molecular Modelling: AMBER, CHARMM, GROMACS, Sybyl, Accelrys NAMD

·         Ab-initio methods: MOPAC, GAMESS, Gaussian

·         Biomolecular Docking: DOCK6

·         Microarray Data Analysis: Cluster

·         Gene Finding Algorithms: TMHMM, Genscan, Glimmer, Prodigal

 

·         Genome Alignment: MUMMER, MGA, LAGAN, mauve, Murasak

 

·         Repeat finding tools: mRep, Phobos, repeatMasker, TRF, tandemscan

 

·         RNA analysis algorithm: RNAmmer, tRNAscan, Vienna RNA

 

          IV.        SOFTWARE LICENSES

 

Following Molecular Modelling facilities need licenses:-

·         The Amber license Agreement is a legal agreement between the end user (either an individual or an entity) and the University of California.

o   AMBER : Users who wish to use AMBER should adhere and follow AMBER License as given in below Link.

o   License : http://ambermd.org/amber11.license.html

 

·         Academic users can obtain CHARMM by contacting The CHARMM Development Project. For-profit companies should contact Accelrys Inc.

o   CHARMM : Users who wish to use CHARMM should adhere and follow CHARMM License as given in below Link.

o   License : http://www.charmm.org/package/license.html

           V.        BRAF ACADEMIC REGISTRATION FORM

 

·         Available at - http://bioinfo-portal.cdac.in/braf_forms/RegistrationForm_Academics.pdf

·         The complete registration form should be faxed to 020-25694084

 

·         For any queries, users can send an email to braf-help@cdac.in

 

          VI.        ACCESS FOR INDUSTRIAL USERS

BRAF is accessible to industrial users on case to case basis and in the mode of contract research projects.

B.   OTHER BIOINFORMATICS FACILITIES (or PRODUCTS) by C-DAC

Some other Bio-Informatics facilities (or Products) with C-DAC are as under:-

 

                      I.        ANVAYA - Workflow Environment for high-throughput genome analysis - (Reference - http://bioinfo-portal.cdac.in/anvaya.html )

Comprehensive analysis of heterogeneous genomic data requires a flexible platform for running complex queries that is capable of integrating and analyzing large amount of genomic data in pipeline.

Anvaya Distribution and Usage:-

·         Free Download Client Installer is available at the site.

·         The client will interact with pre-installed server on C-DAC's BRAF facility (In the downloaded client, ensure Server and Proxy settings are properly done)

·         Kindly Register for dedicated login account. For trial purpose use guest account (login: guest, password: gue2Anv)

·         Login account will be valid for 6 months duration by default and may be extended on further request

 

                    II.        MORE C-DAC Products for BIO-INFORMATICS can be accessed at:-

http://bioinfo-portal.cdac.in/products.html

FOLDIT - AN INNOVATIVE WAY

Protein Folding Problem of Scientific Community in a Computer Game

 

Change in shape of the proteins attribute to biochemical explanation of biological functions. May it be understanding different pathways (series of biochemical reactions) or may be understanding the nature of virus attack, the way the proteins change shape play critical role. Therefore, understanding of protein structure is important for biologists. But, at the same time, it is an extremely complicated task. Further, to simulate the change in the shape of proteins in a dynamically changing environment is a much more difficult task. Today, researchers across the world are trying to achieve perfection in understanding behavior of shapes of proteins (commonly referred as 'Protein Folding Problem').

On the web, there is a protein folding game called Foldit with real protein sequences in three dimensions. Foldit was developed by a large group of researchers who are interested in protein folding. Interestingly, at times humans have done better in folding proteins than computers. This is an innovative move in the area of computer games. The real problems of science would be attempted by zealous community interested in computer games.  

Further details on 'The Science Behind Foldit' can be accessed at:-

http://fold.it/portal/info/about

Foldit can be downloaded from the following website:-

http://fold.it/portal/

Frequently Asked Question on Foldit website are given in the following web page:-

http://fold.it/portal/info/faq

FolditForum

http://fold.it/portal/forum/5

List of the players of Foldit with profiles are listed in the web page:-

http://fold.it/portal/players/profs

In the above link (listing profile of the players), it can be observed that passionate minds are coming from cross-functional background to play Foldit. Probably, this is a dream come true for intellectual community. Success of the promising game (Foldit) may encourage the portal management to innovate with other possibilities to attract more and more passionate people from all walks of life. In the present form, the portal may help in promoting researchers in remote and underdeveloped areas to network and contribute at international level. Let us wish all the very best to Foldit.