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BIOINFORMATICS- CURRENT SCENARIO

 
 
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.
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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.
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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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