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LABORATORY SETUP
  • One Bench top cold centrifuge.
  • One Thermocycler (Amersham Biosciences) [48 well]
  • Tissue Culture set up with one Laminar Air Flow Cabinet.
  • Autoclave.
  • Biochemistry laboratory (fully equipped).
  • Vertical and Submarine gel apparatus.
  • Research
    The newly developed facility of “The Biome” at Salt Lake City Sector 1 Kolkata has paved a new area of Bioinformatics Research. The main focus areas of research in Bioinformatics currently is focused but not restricted to the following :
    (A) Next Generation Sequencing Data Analyses :
    Next Generation sequencing has resulted in the ushering of a new era into bioinformatics research – due to its huge volume of data that is generated out of a single cycle of experiments. The analyst at The Biome has taken up the challenge head on and has made themselves at par with leading research labs around the world.

    Our specializations include : data analyses and annotation of genome and transcriptome analyses experiments as well as subsequent pathway analyses including analyses of differential gene expression patterns.
    (B) The Rare Infectious Disease Initiative :
    The recent outbreak of Ebola has prompted the disease research team of The Biome to undertake structural and interactomic analyses experiments involving proteins encoded by the Ebola Genome.
    (C) The Database Development Initiative :
    The database development team of the Biome is currently involved in preparing a database on Drought and Salinity Stress associated microRNAs in crop plants of the Indian subcontinent.
    Services Offered
  • Next generation sequencing data analyses & genome analyses
  • Sequence analyses (pattern matching)
  • Molecular modelling
  • Structural analyses
  • Molecular dynamic simulations
  • Epitope detection & geometry identification
  • Svm based feature selection
  • Statistical analyses: [ca, pca, anova, c-r, hmms]
  • Virtual screening
  • Available Resources
  • The centre is currently equipped with 10 independent terminals each with Windows XP and UBUNTU Linux operating systems.
  • Independent Internet facility >2MBPS connectivity is available for all the terminals.
  • Apart from these hardware resources, the centre possesses numerous state of art software used in bioinformatics analyses.
  • SL SOFTWARE DESCRIPTION LICENSE
    NGS – DATA ANALYSES PACKAGE
    1 Samtools Standalone Open Source
    2 Bamtools Standalone Open Source
    3 Bowtie Standalone Open Source
    4 Galaxy Cloud Based Open Source (Registration)
    5 Fastqc Standalone Open Source
    6 Velvet Standalone Open Source
    7 Varscan Standalone Open Source
    8 Phase Standalone Open Source
    MOLECULAR MODELING
    9 Modeller 9.14 Standalone Academic License
    10 Yasara Standalone Academic License
    SIMULATION
    11 Gromacs Standalone Academic License
    12 Cabs – Flex Server Academic License
    DOCKING
    13 Autodock Standalone Academic License
    14 Flex - X Standalone Perpetual Academic License*
    15 Hex Standalone Open Source
    SOFTWARE PACKAGE
    16 CLC Workbench Standalone Perpetual Academic License*
    17 Matlab Standalone Perpetual Academic License*
    18 Blast2go Standalone Academic License*
    *All perpetual academic licenses are single user ones.
    Inhouse Software And Tools Developed
    (A) Motdet :
    A tool for detection of conserved residues in amino acid and nucleic acid sequences using clustering and neighbor joining methods with a background position specific scoring matrix. Written and executed in cgi – PERL.
    (B) Text Miner :
    A web based application for the mining of bibliographic data using a combination of text based keywords. The application provides the user with a keyword based search interface and a suggestive list of keywords. It then searches across major bibliographic databases and journal homepages.
     
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