| India had a head start in the field in the 1950’s and the
1960’s thanks to the efforts of G.N. Ramachandran and his
colleagues. At that time all the massive calculations were done
manually. This was an era of individual excellence. However, the
research in the field of Computational Biology saw a major setback
in the 1970s and the 1980s when export of world class computers to
India was not allowed. The computer technology changed in the 1990s
obviating the need for large main frame computers. Also, with the
development of macromolecular crystallography, and sequencing to a
lesser extent, an ambience of handling locally generated data got
established. The 1990s was the era of developing basic
infrastructure and trained human resources with basic skills in the
field of bioinformatics, in which DBT played a prominent role. Data
bases and web based software also began to be developed. The first
decade of this century has seen some quality research being done in
the field as evident from publications, though we are still behind
the world’s standards. With the infrastructure now in place through
BTISnet, India is now geared to do some landmark research in the
field. Future challenge for the country is to develop major
bioinformatics support required to handle the massive datasets now
being generated by the new generation high-throughput technologies.
Also is it becoming essential to bridge the gap between
bioinformaticians and experimental biologists by bringing their
expertise together through interdisciplinary projects and breeding a
newer generation of scientists who are well trained in both
fields. |
| |
| BIOTECHNOLOGY INFORMATION SYSTEM NETWORK
(BTISNET) |
| The Biotechnology Information System Network (BTISnet) of
the Department of biotechnology is spread across the county with 168
centres. The network centres are in various levels and include
centres of excellence (CoE), distributed information centres (DIC),
distributed information sub centres (Sub DIC) and bioinformatics
infrastructure facilities (BIF). The network houses the
Supercomputer Facility for Bioinformatics and Interactive Graphics
Facility. Large numbers of R&D projects in bioinformatics are
also being supported through this programme. The network supports
teaching program in M.Sc, M.Tech and PhD in Bioinformatics and
Computational Biology to generate skilled manpower in
Bioinformatics. Further, the BTISnet centres are conducting short
term trainings/ workshops for the benefit of research community
including experimental biologists. These centres also provide
services to the scientific community. These activities are being
coordinated by the Apex BTIC which is located in the DBT head
quarter. A map showing the location of these centres is as follows. |
 |
| |
| Centres of Excellence (CoE): |
| Six Centre of Excellence (CoE) in Bioinformatics and
Computational Biology have been established as part of BTISnet.
These Centres are well equipped with State of Art Bioinformatics
infrastructure to support research within the Institute as well as
neighbouring institutions. The focus of these centres is high
quality research education and services. The Bose Institute, Kolkata
has been recognised as CoE for under taking research in the area of
modelling of proteins structures and interaction; molecular
interaction and docking; drug design; chromosomal dynamics;
evolutionally systems biology; developing tools for analysing deep
sequencing data. The centre has developed 4 web servers focusing on
the above mention areas: Proface, InteGeom, ConfPlot, ContPlot. The
centre provides services in the area of genome/protein analysis,
protein structure and drug designing. The thrust areas for research
for the CoE at IISc, Bangalore are systems biology, structural
biology and bioinformatics, molecular design, molecular modelling,
structural pharmacology and computational immunology. The centre has
developed some software’s for structural biology (such as CSSP,
MIPS, FAIR and SSMBS). The centre supports Interactive graphics
facilities. The centre is offering 3 PhD courses viz.
Bioinformatics, computational approaches to drug discovery,
chemoinformatics. The research focus of the CoE at JNU, New Delhi is
towards the application of computational biology in pathogenic
diseases like Mycobacterium, Leishmani, Malaria, etc. The centre has
also signed MoU with Bioinformatics Institute, Singapore for
academic and research collaboration. The main activity of the centre
at MKU, Madurai focuses on research and providing services in the
areas of structural bioinformatics, proteomics, creation of
database, data mining, molecular modelling, dynamics and computer
aided drug design. The centre provides consultancy to the industry.
Further, it also provides easy accessibility to databases and
software tools, and also guidance for utilization these tools to
other academic institutions. The CoE at Pune University focuses on
genomics, protemics and phylogenetic analysis of infectious viruses
such mumps, rhinovirus, Dengue etc. The centre has developed
database for these viruses which include Viral protein structure
database, Antigen- Antibody Interaction Database and Virgen. Further
the centre have develop server for genotyping of mumps viruses, sub
typing dengue viruses, and World’s first server for prediction
antibody-binding sites of protein antigens. |
| |
| Distributed Information Centre (DIC): |
| Eleven Distributed Information Centre (DIC)in
Bioinformatics and Computational Biology have been established as
part of BTISnet. The focus of these centres, like CoEs is high
quality research, education and services. The DICS at IARI, New
Delhi and Kerala agricultural University, Thrissur are mainly
focused on Agri-informatics. At IARI web based tool like Wheat
Informatics, MiRule (Rule based micro RNA prediction Tool), a plant
Transmembrane Kinase prediction tool have been developed. The centre
is offering PG course in areas of ‘Simulation and Informatics’. The
centre provides training for agricultural scientist staff and
students. The recent research focus of NII, New Delhi centre is on
prediction of micoRNAs and their protein interaction partners, and
bioinformatics analysis of enzymes involved in biosynthesis of
lantibiotics and cycodipeptides. Some of the database and software
package developed at NII include prediction of PDZ binding peptides,
Analysis of PKS/NRPS, Motif Discovery. The thrust area for the
centre at University of Calcutta, Kolkata is human resource
development for the east and north east region of the country. For
this purpose the centre is offering 2 courses viz. MSc in
Bioinformatics and Biophysics and advance PG diploma in
Bioinformatics. The centre at Anna University is mainly focusing
research in the area of Molecular Dynamics, Cluster computing,
Enzyme structure function studies, protein interactions, comparative
Genomics and system Biology. A project on setting up of mirror site
on electronic database and biological software in public was funded
under Jai Vigyan National Science and Technology Mission to IMTECH,
Chandigarh. The centre has mirrored number of sites including Public
Domain Software in Biology like software at EBI and Indiana
university; and General Purpose Software Packages such as GNU
Project web server and PostgreSQL Site. The major activity now days
at IMTECH is to create the electronic database of biological
resources in public domain and to distribute these resources on-line
as well as off-line and these will be searchable through email. The
public domain resources in biology has been divided in three
categories i) Public Domain Software in Biology (PDSB); ii) Public
Domain Web Servers in Biology (PDWSB); iii) Public Domain Web Pages
Biology (PDWPB). |
| |
| Sub-Distributed Information Centre
(DISCs): |
| Fifty Sub-DICs have been established at various
Institutions/ Universities. These centres were mainly established
with the aim to provide service to the research community. However
these centres are now also imparting training in bioinformatics
through workshops. Many centres have now ventured in bioinformatics
related R&D activities and have also developed information
resources in the form of Databases. |
| |
| Bioinformatics Infrastructure Facilities
(BIFs): |
| The aim of these centres is biology and biotechnology
teaching through bioinformatics. The scheme is designed to expose
teachers, scientists and students to the use of bioinformatics in
solving hard core biological problems. The centres use lecture
materials, video clippings, demonstrations, tutorials and online
facilities for teaching. Hundred and one educational institutions
have so far been supported under this scheme and some more are in
pipeline. |
| |
| BTISnet website: |
| The BTISnet website with URL http:// www.btisnet.gov.in provides a central resource to all the bioinformatics centres in
respect of the work done by each one of them in the area of
bioinformatics. Through this site, the BTIC provides all information
such as budget release, status of submission of accounts and
progress report by the BTISnet Centres. The site provides a list of
open access journals, details of the fellowships provided through
the bioinformatics division like BINC, studentship and traineeship,
access to online lecture portals and their links, announcements of
the national bioinformatics coordinators meetings and its
proceedings, bioinformatics publications from India and the
bioinformatics resources like software and databases. A snapshot of
the website is under. |
 |
| |
| Coordinator’s Meeting of Biotechnology Information System
Network (BTISnet): |
| The progress of these Centres is annually reviewed and in
this series the 24th Coordinator’s Meeting will be
organised in CIMAP, Lucknow on 3-4th Feb 2013. |
| |
| North Eastern Bioinformatics Network
(NEBInet): |
| Under the special drive to strengthen the North
Easten States of the Country a Bioinformatics network ‘NEBInet’
consisting of 29 Bioinformatics centers was established across 8
states. NEBInet has 1 DIC (at NEHU), 2 DISCs (at IBSD, and Sikkim
State Council of Science and Technology) and 26 BIFs (at various
universities, colleges and institutions). In order to monitor the
progress these centre and ascertain their difficulties
5th interactive meeting of the 29 centre, coordinator
meeting was organised in Aizwal, Mizoram in October 2012. The
meeting was attended by Higher and Technical education, Government
of Mizoram. A snap of the meeting is as follows.
|
 |
| |
| Supercomputing Facility (SCFBio, IIT
Delhi): |
| A highend data centre with multi-tera facility has
been established at IIT, Delhi. This facility is accessed by student
and scientists all over the country. With the vision to develop
personalised medicine using Gene-to-Drug pathway in an
automated mode, particularly to cut the cost, time and effort
involved in drug discovery and also to decipher the molecular level
principles in the process, IIT, Delhi has under taken the endeavour
to develop softwares to design lead molecule which can be improved
in combination with experiments to yield personalised medicine. The
efforts have resulted in a whole genome analysis methodology and
software based on DNA energetics (ChemGenome), an all atom
energy based computational protocol for protein tertiary structure
prediction (Bhageerath and Bhageerath-H) and a binding free
energy based methodology for protein/DNA targeted lead molecule
design (Sanjeevini). Leadinvent incubated at IIT Delhi form
2006 to 2009 and Novoinformatics under incubation at IIT Delhi since
April 2011 are two start-up companies created by the students and
staff of SCFBio based on the Gene-to-Drug innovations at
SCFBio, IIT Delhi. |
| |
| HUMAN
RESOURCE DEVELOPMENT IN BIOINFORMATICS, COMPUTATIONAL AND SYSTEMS
BIOLOGY |
| Bioinformatics is an emerging interdisciplinary area of
biotechnology and encompasses systematic development and application
of IT solutions to handle biological research problems. Areas such
as proteomics, genomics, combinatorial chemistry, statistics,
nanotechnology, spectroscopy and structural and computational
biology will have increasing applications of Bioinformatics in days
to come. To handle all these biological research problems, it
requires highly trained manpower to deal molecular biology and
application of software tools. The department had accorded this area
high priority and has introduced several innovative educational
activities to meet the present requirements including several
long-term and short-term educational programs to address this gap.
The details are as follows: |
| |
| M. Sc.
Network Program, M.Tech, Advanced P.G. Diploma Courses & Ph.D.
Program in Bioinformatics: |
| The MKU,
Madurai, Pondicherry University, Pondicherry and Anna University,
Chennai have initiated a Network programme on higher education in
“M.Sc. Computational Biology” on consortium basis. The classes are
being conducted through video conferencing and virtual class room
approaches. The objective of the network programme is to share the
expertise of teachers as well as the resources which are created by
the BTISnet Centres. The program envisages creating of a strong
computational and experimental basis to bioinformatics education at
the post graduate level. The other universities i.e. i) JNU, New
Delhi ii) Pune University, Pune and iii) Calcutta University,
Kolkatta are continuing M.Tech., M.Sc. and Post Graduate diploma
courses in bioinformatics, respectively. This year more than 70
students have graduated from these programs. The CoEs of BTISnet
including the super-computing facility at IIT, New Delhi are running
Ph.D. programs in Bioinformatics to meet the huge requirement for
high-end human resource in Bioinformatics and Computational
Biology. |
|
|
| Short Term
Training Programs: |
| Basic
understanding and hands on experience in the area of Bioinformatics
is provided to the researchers and students, by each of the BTISnet
Centre by conducting one or more short term training programmes each
year. A schedule of the training programmes conducted by BTISNet
Centres is published in the form of annual training calendar each
year by the Department. This calender is distributed to all
institutes, and is also available at the btisnet website. The
BTISnet centres have organized more than 100 short-term training
during the year 2012-13 with focus on a broad spectrum of areas such
as NGS analysis, drug discovery, protein folding, chemo-informatics
etc. |
 |
| |
| Bioinformatics National Certification Examination
(BINC): |
| The BINC examination was introduced in 2005 by the
Department of Biotechnology (DBT), Government of India to certify
professionals in the area of Bioinformatics. JNU, New Delhi is
conducting the BINC exam from 2011 onwards. The BINC National
Coordination committee is the driving force in setting and
maintaining high standards of the BINC examination. The examination
is conducted at eight centers (http://binc.scisjnu.ernet.in/).
The exam employs a three-tier system including an objective,
subjective and practical examination. The fellowship provided is at
par with NET, GATE, BET national Exams. So far 85 candidates have
qualified the BINC and 15 out of them are availing the
fellowship. |
| |
| BIOINFORMATICS R&D ACTIVITIES |
| |
| Establishment of national rice resource database: |
| Two distinct activities have been initiated to formulate
this database. The first activity is being coordinated by the NBPGR,
New Delhi with participation of NRCPB, New Delhi; CRRI, Cuttak; DRR,
Hyderabad; CSSRI, Karnal; IGKV, Raipur and BHU, Varanasi in
multicentric mode. This activity aims at characterization of rice
germplasm based on agronomic traits so as to form a core/mini-core
germplasm. Subsequently, the unique collection of germplasm would be
characterized in detail at molecular level to generate passport
data. The second activity is being carried out by University of
Delhi, South campus and will aims at compiling data on whole genome
sequence/proteome of rice and a huge collection of experimental data
generated over several decades. |
| |
| Establishment of national database on
Tuberculosis: |
| This database has been developed in a multi-centric mode.
The layout of this database has been designed by NJIL&OMID, Agra
in first phase of the project and it is now being implemented
simultaneously at NJIL&OMD, Agra and MANIT, Bhopal. MANIT has
created on online data warehouse for storage of biological data,
developed tools for data-mining etc. and is also providing technical
support to participating institutions. NTI, Bangalore is providing
input in the areas of epidemiological, sociological issues in
addition to monitoring of revised RNTCP programme. IOB, Bangalore
has its input in the form of a TB-NET portal, web resource for
proteomic, host-pathogen interaction and building up pathway
resources. JNU, New Delhi will be giving incepts through the MGDD
database and its up gradation. IISC, Bangalore has developed the
database from system level modelling and genome profiling of MTB. In
addition, structural bioinformatics analysis and methodologies for
genotype- phenotype mapping is being done by IISc. TRC, Chennai is
annotating the genomes of mycobacteriophages, under study and is
also developing bioinformatics tools for analysis of the
database. |
| |
| Indo-Japan Collaboration in
Bioinformatics: |
| DBT, India and AIST, Japan had signed an MoU in the month
of February, 2007 to work jointly in the field of Biotechnology,
which has recently been extended for another 5 yrs. In the first
instance, it was decided to work in the area of Bioinformatics and
Computational biology. Four challenging themes viz. (1) Designing
potential targets in membrane proteins, (2) Designing GPCRs
Mimetics, (3) Designing FIXER for disorders, and (4) Designing
cybrog lectins were identified. The proposals were implemented in
collaboration with the CBRC group of AIST, Tokyo. The project at
Manonmaniam Sundaranar University, Tirunelveli focusses mainly on the
carbohydrade-hemagglutinin complexes of Influenza A virus and
designing cyborg lectin by mutating the important amino-acid
residues. The overall conformation and hydrogen bonding patterns of
4 biologically important sialydisaccharide have been deciphered. The
binding specificity of 4 hemagglutinin lectins of influenza-A virus
and 6 biologically important sialydisaccharide have been studied.
Mutation studies in the active site of wheat germ agglutinin have
been carried out and a promising mutant has been identified by
in-silico methods. This cyborg lectin can be used for targeted drug
delivery and biological cell marker in cancer therapeutics. The
project has resulted in two high impact factor joint publications.
The second project on Genome wide survey of olfactory receptors in
diverse eukaryotic model organisms is being implemented at NCBS,
Bangalore and Bharathidasan University. The project has led to the
development of a software to identify olfactory receptors (OR) from
whole genomes of organisms. This TM-MODIF software has been
published and will be distributed for academic purposes soon.
Further, an exhaustive database on ORs comprising of sequences
cluster analysis data, 3D structure of more 800 ORs, mutations and
their effect on odour response, predicted dimer interface has been
developed and would be released on public domain after publication.
The third project at University of Madras and SRM University is on
identification of efflux pump inhibitors to gram-negative organism
using bioinformatics tools, in vitro analyses and crystallographic
studies. In an attempt to identify efflux pump inhibitors to gram
negative organism the computational structural analysis of two pumps
ArcB and MexB was done. Through virtual screening and in vitro
assays for validation, two promising inhibitors viz. quercetin and
thionine were identified. In-vitro testing of another 100 putative
inhibitors is under progress. In fourth project on Designing cyborg
lectins based on subunit-association in jacalin-type lectins at NCL,
Pune attempt is being made to design cyborg (artificial) tetrameric
lectins which can act as a carrier for a peptide-like drug molecule
and can also recognize cells through their sugar binding capacity, a
functional requirement for a carrier molecule in targeted drug
delivery. Several joint publications in indexed journals have
resulted from this collaboration. |
| Bilateral Indo-Japan Workshop was
organized in Hyderabad in November 2008. It was agreed to evolve
projects in the field of Glycoscience, Biomarker and Cell
Engineering in the next phase of corporation. Since then, four
projects have been supported in the area of cell engineering
focusing mainly on senescence and cell proliferation, with the aim
to understand cancers and develop novel ways for intervention. The
projects employ molecular biology and system biology approach.
Objective of one of the projects is to develop Ashwagandha derived
phytochemicals for differentiation-based therapy of brain cancers.
Another complementary project aims at developing mass propagation
for Ashwagandha and also standardize a protocol for development of
Ashwagandha transgenics to understand metabolite accumulation and
transport. |
| |
| R&D project supported under competitive grant
scheme: |
The first R&D proposal in bioinformatics was received by the
department in 1999. Since then the division has supported 97
projects of which 29 are ongoing and 10 are in pipeline. Over the
years the projects have been supported in various areas such as drug
and inhibitor designing through molecular modelling; development of
tools for genome/microarray databases/protein structure analysis;
development of database of biological importance; better algorithms
for imaging; tools for deciphering genes and pathways involved in
diseases; tools and database for efficient disease management and
Agri-informatics. Over the years a general shift in trend in
Bioinformatics research has been observed. In early 2000 most of the
projects funded focussed on using existing tools for solving
problems in Agriculture and Medical Science. In some projects novel
algorithms, tools and software were developed particularly for
protein structure analysis. However, biological validation component
in these projects was non-existent. The project now being supported
focus on developing novel tools with strong experimental validation
component. In the project at MKU, Madhuri work has been initiated
for the construction of a potent computational platform for the
identification of non-coding small RNAs (sRNAs) and small ORFs
(sORFs); experimental validation of predicted sRNAs/sORFs, and their
functional characterization. In another project at Bose
Institute, Kolkata, investigators are trying to gain mechanistic
insight into the role of conformational modulations in driving BC12s
apoptotic network for eventual use in therapeutic design. The
project at NISER, Bhubneswar, aims at understanding of kinase
inhibiters by applying a molecular docking and pathway profiling
approach so that novel kinase inhibitors which are specific for a
kinase or for a particular set of kinase depending on its pathway
can be designed. Development of internet computing engines and
knowledgebase for the analysis of protein sequences and structures
is being carried out at IISc, Bangalore. The project being carried
out at NCL, Pune aims at reconstruction of different metabolic and
signalling pathways involved in immune cells (specifically, T-cells)
and cancer cells (specifically, Glioma), and to find the key
metabolites, reactions or immune-stimulators, for controlling
cancer.A number of projects funded in last 3 years aim at
developing novel tools for the robust analysis of voluminous data
being generated through the ‘omics’ approach. The project at NDRI,
Karnal and IASRI, New Delhi on ‘Buffalo Genome
Information Resource’ focusses on designing and
developing buffalo genome database and maintaining gene annotations
and revealing the underlying mechanism of chromosomal evolution
between cattle and buffalo. Another proposal at IARI, New Delhi aims
at development of a comprehensive genomic resource and knowledge
base of two plant parasitic nematodes, Meloidogyne
graminicola and Heterodera avenae, important nematode
problems of rice and wheat respectively worldwide. The joint project
being implemented at Birla Institute of Technology, Mesra, Ranchi,
and Chaudhary Charan Singh University, Meerut aims at discovery,
annotation, validation and characterization of SNPs in Wheat
(Triticum aestivum L.) using Next-Generation Sequencing Data.
These SNPs may be used for construction of high density genetic and
physical maps of bread wheat, and the maps in their turn may be
utilized for various purposes including high resolution genetic
mapping of the QTLs/genes for desirable traits leading to positional
cloning of these QTLs/genes. |
| |
| OTHER ACTIVITIES OF Bioinformatics
Division: |
| |
| Bioinformatics and Computational Biology – A Compendium
of Research Publications from India: |
| In an attempt to collate peer reviewed research
publications from India on Bioinformatics and Computational Biology,
the department has made an effort in association with Prof. M
Vijayan, Chairman of the Task Force and compiled a research
publication compendium in this area form the year 2002-2010. Over
2000 publications have been compiled from various sources and
published as a booklet. |
| |
| Networking of DBT Institute National knowledge
Network: |
| Fourteen DBT institutes have been networked through high
speed connectively of NKN. This network would allow implementation
of major consortium projects by the institution. The expenditure for
the same witlbe met out though NKN program and institute need not
make any payments. |
| |
| Compliance to IPV6: |
| DBT and its autonomous institutes are made compliant for
switching over to IPV6 so as to benefit the advantages of new
version. |
| |
| Innovative Young Biotechnologist Award
(IYBA): |
| The Bioinformatics group is also coordinating for the
IYBA and so far 86 young scientists have availed this award to carry
out independent innovative research in Biological
sciences. |
| |
| Conferences, Travel, Exhibition and popular lecture
(CTEP): |
| The CETP online program for support to Conferences,
Travel, Exhibition and popular lecture has become quite popular
among the stake holders. On an average 100 travel fellowships are
being supported for the scientists to travel abroad for presenting
their papers. Improved governance has been possible because of this
program as the budget disbursement is also carryout through online
system. |
| |
| DBT e-Library Consortium (DeLCON): |
| All DBT Institutes and 18 NER Institutes are part of
DeLCON and they have access to over 900 high impact e-journals. The
site can be seen at http://delcon.gov.in/. |
| |
| For more details on BTISnet
please visit http://www.btisnet.gov.in/ |
| |
| Important Websites of DBT |
| |
| |
| Department of Biotechnology, Government of India |
| |
| |
| Biotechnology Informtion System Network |
| |
| |
| Online Submission & Monitoring System (CTEP) |
| |
| |
| DBT E-Library Consortium (DeLCON) |
| |
| |
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