Sunday, 31 March 2013

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.


 
·         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.



           V.        BRAF ACADEMIC REGISTRATION FORM
 

·         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:-

No comments:

Post a Comment