(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
·
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:-
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