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Jute genome project md lashkar

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  • 1. SWAPNOJAATRA Jute Genome Project The Journey & What's happening NOW
  • 2.
    • The Jute Genome Project
    • Quick Facts
    • JuteGenome is a project of “Swapnojaatra” , a Biotech Team
    • JGP is a Three Party Joint venture, Dec 2009-Dec2010
    • A mesh of local Skills & foreign Hi-Tech Lab Services
    • Funded by Ministry of Agriculture ( 50% home, 50% abroad)
    • Executed/Managed by DataSoft Systems BD Ltd
      • Program Manager (s)
      • 15 IT Professionals
      • 10 Molecular Biologist
      • 9 Plant Biologist
  • 3.
    • The Jute Genome Project
    • Quick Facts (Continued)
    • Phase -I did not have much to do with BJRI –Team
    • Jute Genome Draft Completed on June 16 th
    • Still more work to do, complete by December 31 st
    • Phase-II, a 3 year project Launched by GoB under BJRI label
    • SJ feels the need to “Open Up” and entertain new project Requests
  • 4. Detail Dive The Team & Initial Challenges 1. Best Students from Dept of Genetic Engineering, Molecular Biology ( aka Dr. Haseena’s & Dr. Jeba’s Lab Students) 2. A group of Seasoned and daredevil IT professionals from DataSoft 3. Funding was not ready but must start on first Week of Jan to meet the dateline ….. DataSoft stepped in. Overseas & Media communication 4. REAL CHALLENGE : 2 Team Spoke two different languages
  • 5.
    • Detail Dive
    • Moving on to One Language
    • Class room kind of Sitting Arrangements …( Laptops & Projectors)
    • All Open Source Tools ( Linux, Php, MySQL, Bio-Tools)
    • X-Training & Team Building
    IT –Team: Bio-Team: Linux Basic Commands Perl Presentation... MySQL Workshop File System /Mount points The Application for Forum GENEMARK MUMmer Non-coding RNA annotation PASA SNAP TMHMM & signalP
  • 6.
    • Detail Dive
    • Other Challenges
    • Work hours
    • The NDA
    • Continuously Changing Directions
    • MAC-Attacks on Weekends
    • Communication protocol with external Teams
    • Lack of Funding for Computation
  • 7. The Challenge What makes us Different
  • 8. The Challenge What makes the Crops Different
  • 9. The Blue Print & the Building Blocks
  • 10. What is Genome Sequencing Genome Sequencing means reading the whole story of life just like reading a book- chapter by chapter
  • 11. Bringing Bio to IT High performing Sequencers decode Randomly Broken sequences of A T C G from extracted DNA
  • 12. Bringing Bio to IT
  • 13. Bringing Bio to IT
    • ASSEMBLE  Repeat Masking  Jumble of ACGT jumble of alphabets!!
    • Extrons
    • Introns
  • 14. Our Expertise Our Tools Assembly*: 454 GS FLX, Illumina/Solexa, and SOLiD with Newbler/CLC-Bio Repeat Analysis: Repeat Masker, Repeat Modeling Annotation : Machine/ Manual Using Commercial Compliance Cloud: Augustus, genewise, Twinscan  Manual Curation:  Web or Desktop application Publishing: gbrowse
  • 15. SWAPNOJAATRA What we been Doing Research: Analysis of PXE disease, its association with ABCC6 and GGCX genes and their comparison. Computational drug design approach against two pathogens; Vibrio cholerae and Streptococcus pneumoniae. Publications: Molecular docking study of capsular regulatory protein in S. pneumoniae portends the novel approach to its treatment, Thapa S, Zubaer A, 2011, Open Access Bioinformatics (Accepted) Palindromes drive re-assortment in Influenza A, Zubaer A, Thapa S, 2011, Bioinformation 7(3); 115-119.
  • 16.
    • SWAPNOJAATRA
    • Potential Areas of Engagement
    • Genome Pipeline “One-Stop Service” is a niche market that spreads across the globe... We can lineup Collaborators
    • Local Pharma industries will be exploring many areas of Bioinformatics near 2012 and can become our subscriber or partner for joint ventures
    • Offer Bioinformatics Trainings to Educational Institutions
  • 17. SWAPNOJAATRA Next Move We need to Open Up .. Create a Platform …. A Consortium so that it can facilitate Students ……. More details later .
  • 18. SWAPNOJAATRA Thank You ?