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a database for Mycobacterium secretome analysis
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The NBU Bioinformatics Facility was established in November 2006 with the help of the grant from DBT (Department of Biotechnology, Govt. of India). Since then we have marched forward steadily. The centre has every modern facility of information and communication including necessary hardware and software. The centre provides access to the faculty members, research scholars and students from nearby universities, colleges and research institutions interested in working in the field of bioinformatics. The Coordinator’s group is actively engaged in research in the field of genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria. Codon usage analysis, biological sequence analysis, Protein structure prediction, phylogenetic study, molecular modeling and molecular docking are the major thrust areas. NBU Bioinformatics Facility boasts of having Frankia genome sequencing project in collaboration with the Department of Microbiology, University of New Hampshire, USA. There are a number of publications in national and international journals. Full paper and posters have been presented in various national and international conferences on the relevant areas.

Summary of the progress made by the centre

Since its inception in 2006, NBU Bif facility has made considerable progress. In this short span of time, the centre has established itself as primer bioinformatics research institute in eastern India. It caters to the needs of students from North Bengal, Sikkim, Eastern part of Bihar and even neighboring countries like Nepal, Bhutan and Bangladesh. 28 Research Publications on hardcore bioinformatics have been published in various national and international peer-reviewed journals. The centre has developed software for Codon analysis and Triplet-based phylogenetic studies. Several databases are being currently developed.

Major research activities in Biotechnology and its related fields

At NBU major research activities are clustered around the fields of molecular genetics, microbial biotechnology, plant tissue culture, immunology, microbial genomics, transgenics, genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria.

Area of specialization of the centre

Bioinformatics, microbial genomics, molecular modeling, molecular phylogeny etc.

Major activities of the centre

Nine National-level workshops on Bioinformatics have been conducted covering topics like biodiversity informatics, database, alignment tools, phylogeny software, molecular evolution, homology modeling . Along with that Regional workshop on bioinformatics has been carried out in various colleges of North Bengal to popularize bioinformatics amongst college students’ .The Coordinator Dr. Arnab Sen has set up International collaboration with the University of New Hampshire, USA. He along with Prof. Louis Tisa (Department of Microbiology, UNH, USA) has been working towards complete genome sequencing of five Frankia strains. Considerable amount of work relating to the characterization of bacteria on the basis of codon usage and phylogeny has been done and are expected to be published in the coming days. Established a connection with the Grid Computing environment of CDAC Pune and having access to PARAM-PADMA Supercomputing facility for Bioinformatics research and applications. The centre periodically publishes a newsletter of the NBU Bioinformatics Facility called “BIOINFOLINE” (ISSN No. 0974-9403).

Infrastructure facilities in the Bioinformatics Centre

Computer and communication: 10 PCs with OS One High end server and a Medium end server Scientific and Software packages: Two Windows 2003 Server with license, 10 Windows XP Professional with license, Microsoft ISA Server 2005 for Proxy Server, one Microsoft Visual Studio, .NET, MS SQL Server (Std.), MS Office 2003, 10 Quick Heal AVG Antivirus Package. Acclerys Gene, GENOME BROWSER, CODONS, CODON W, Cn3D, MODELLER 9v6, CLUSTAL W, CLUSTAL X, DNAsp 4.0, MEGA 4.0, TREEVIEW, SPDBV, VMD, GROMACS, AUTODOCK, RASMOL, PHYLIP, PAUP, DAMBE, Jcat, Argus Lab, C++ and PERL. Printers: One Laser printer (network), one Desk-Jet printer Other resources: Internet Lease line (256 kbps). One 6 Mbps line from Reliance.

Types of service provided

The centre provides access to the faculty members, research scholars and students from nearby universities, colleges and research institutions interested in working in the field of bioinformatics.

Educational activities with details of placement

One PhD students (Subarna Thakur) is currently engaged in her research work utilizing the facility. Uttam Mandal and Saubashya Sur have submitted their PhD thesis. Besides faculty members, students and research scholars from other departments, institutes and nearby areas utilize this facility.

Collaborative work and initiatives

The Coordinator Dr. Arnab Sen has set up International collaboration with the Department of Microbiology, University of New Hampshire, USA.

Databases and software developed

We have developed programs for codon usage analysis and another for phylogenetic analysis. A database named BAMBOOINFOLINE, a database for North Bengal bamboos (http://www.bamboodb.ind.in/) has been developed.

Objectives of the Centre

  • To establish BIF to support the teaching activities of biology and its allied areas of the host institute in particular and the neighbouring institutions in general.
  • To build up information resources, prepare databases of interest to its users and to develop relevant information handling tools and techniques.
  • To assess information requirements, organize creation of necessary infrastructure and to provide information and computer support services to the users.
  • To establish linkages with BTISnet of DBT for sharing information resources and expertise.
  • To organize training/workshops for familiarizing the applications of Bioinformatics in biology teaching and learning activities.

Future activities:

  • Secretome Analysis of some actinobacteria and pathogenic bacteria like Mycobacterium.
  • Construction of Secretome database of Mycobacterium
  • Annotation and Codon usage analysis of the newly available Frankia genomes
  • Molecular modeling, Molecular Dynamics of some nitrogen fixing proteins and bacterial toxin proteins
  • Database development for medicinal plants of Darjeeling District and Malda district
  • In-silico analysis of Nitric Oxide genes of Frankia, which play an important role in symbiotic association of Frankia
  • Publication of Newsletter and conducting various training programs/workshops and seminar/ conference in bioinformatics in North Bengal and adjoining areas.