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Team India Consortium with Global Partnership. A CSIR-led initiative for affordable healthcare to the developing world. Council of Scientific and Industrial Research INDIA. http://www.osdd.net.

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Team India Consortium with Global Partnership

A CSIR-led initiative for affordable healthcare to the developing world

Council of Scientific and Industrial Research

INDIA

http://www.osdd.net


“When it comes to health, we need to have a balanced view between health as a right and health as a business”

Prof Samir Brahmachari

Director General, CSIR and

Chief Mentor, OSDD

(Ref: Cell (2008) v.133, pp. 201-203)

50


  • One person between

  • every 20 seconds

  • 1.7 Million people

  • every year

  • In India

    • Nearly 1000 people

    • every day

    • Two people

    • every 3 minutes

  • TB Kills

    Image Credits:  Teseum/Flickr


    Deaths between due to Tuberculosis in 2008

    Source: GlobalHealthFacts.org

    • More than 2 billion people (~1/3 of world population) is affected with the

    • tubercle bacilli


    TB Drug between Discovery


    “Generations of advances in research and technology have bypassed TB research”- Anthony Fauci, NIAID .

    “The field has been too isolated and inward-looking” Dr. Margaret Chan, head WHO


    Why open source drug discovery
    Why Open Source Drug discovery ? bypassed TB research”

    • Many eye balls make the bug shallow!

    • Lack of market incentive for TB

    • Successful Open Source Models

      • Human Genome Sequencing Initiative

      • Open Source Software Initiative (eg: Linux OS)

      • Android

      • The WWW


    OSDD Platform bypassed TB research”

    System Architecture

    Collaborative tools to accelerate neglected diseases research” in the book “Collaborative Computational Technologies for Biomedical Research”. Wiley and Sons. 2011 (in press).


    Osdd attribution and ip
    OSDD: Attribution and IP bypassed TB research”

    • All contributions on the OSDD portal attributed to the authors with date and time stamp

    • Real time data sharing

    • Click wrap license agreement

      • All contributions treated as Protected Collective Information

        • mandates sharing,

        • attribution,

        • contribute back


    Osdd view on patents
    OSDD View on Patents bypassed TB research”

    • Two patent applied molecules in hit to lead phase

    • Patentonly to ensure that:

      • Quality assurance in downstream processes

      • Subsequent innovations remain in open source

      • Affordability : through non exclusive licenses


    OSDD – Multipronged approaches bypassed TB research”

    DRUG TARGET BASED

    (18 Drug Targets)

    NATURAL PRODUCT BASED (135 Phytomolecules )

    LIGAND BASED

    (Pubchem Bioassay Data/New inhibitors/)

    Lead Optimization

    Potential hit


    Community peer review open funding review
    Community peer review bypassed TB research”Open Funding Review


    OSDD Open Access Resources bypassed TB research”

    Assembly line for drug discovery

    • I Biological Repository

    • i. Open access clinical strains repository

    • ii. Open access clone repository

    • iii. Open access protein repository

    • II Chemical Repository

    • i. Open access small molecule repository

    • III Open Screening Facility

      • i. Submit your compounds for anti-tuberculosis screening


    Computational Resources developed with bypassed TB research”

    Community participation

    http://tbrowse.osdd.net

    http://sysborg2.osdd.net

    Bhardwaj et al. Tuberculosis (Edinb). 2009 Sep;89(5):386-7

    Bhardwaj et al. 2011 John Wiley & Sons, Inc.

    Chembio Toolkit

    TrapTB

    Mtb drug targets database

    Workflow engine with federated resources

    AmPhyDB

    AntimycobacterialPhytomolecule Database

    Mtb essen\tial genes database


    COG bypassed TB research”

    Easy RNA Profile IdentificatioN

    Database of Conditionally Regulated Proteins

    Pathway network & Unique pathways

    Drug Targets (TDR/Plos/TDI)

    Databases Do not “talk” to each other

    Mycobacterial Genome Divergence Database

    Operon predictions

    (DOOR/VIMSS/Rutherford)

    * This is representative set of post-genomics data available on TB


    COG bypassed TB research”

    Easy RNA Profile IdentificatioN

    Database of Conditionally Regulated Proteins

    Pathway network & Unique pathways

    Drug Targets (TDR/Plos/TDI)

    Databases now do “talk” to each other !!

    Mycobacterial Genome Divergence Database

    Operon predictions

    (DOOR/VIMSS/Rutherford)

    More than 100 datasetsencompassing a million data points


    Publication in Tuberculosis 2009 bypassed TB research”

    AnshuBhardwaj

    DeekshaBhartiya

    VinodScaria

    NitinKumar

    OpenLabNoteBook on SysBorgTB

    http://sysborgtb.osdd.net/bin/view/OpenLabNotebook/TBMapDataset

    Deeksha Bhartiya

    Nitin Kumar


    The bypassed TB research” “Connect to Decode” Programme

    Collaborative Curation

    Curated

    Annotations

    OSDD C2D

    Community

    800+ Student Researchers

    Literature

    Annotation Tools

    Raw

    Annotations

    Pathway/Interactome | Gene Ontology | Protein Structure/Fold | Glycomics| Immunome

    Genomic

    Databases


    “Given enough eyeballs, all bugs are shallow” bypassed TB research”

    -Linus Torvalds

    Errors are Discussed by the Community

    Errors are corrected by the Community

    Errors are marked by the Community for Correction


    Innovative Crowd Sourcing Model for Mtb Systems Biology bypassed TB research”

    Collaborative Curation

    Curated

    Annotations

    Literature

    Annotation Tools

    Raw

    Annotations

    Community of >800 student researchers

    87% of Mtb genome annotated

    Genomic

    Databases

    Generated the largest Interactome & Metabolic Map of Mtb


    Within weeks, 830 volunteered to re-annotate the entire bypassed TB research”M. tuberculosis genome. The work started in December 2009 and was completed by April 2010, packing nearly 300 man-years into 4 months!

    Source: Munos B. Can Open-Source Drug R&D

    Repower Pharmaceutical Innovation?

    Clin Pharmacol Ther 2010;87:534–536

    The Open-Source Drug Discovery (OSDD), which is dedicated to discovering treatments for diseases that plague the developing world, surprised many when more than 400 of its volunteer researchers reannotated the tuberculosis bacterium genome, wiki style, in just 4 months—record time for such an endeavor

    Source: Margie Patlak. Open-Source Science Makes Headway

    J Natl Cancer Inst. 2010 Aug 18;102(16):1221-3


    Nagasuma chandra indian institute of science bangalore
    Nagasuma Chandra, bypassed TB research”Indian Institute of Science, Bangalore


    OSDD SInCRe bypassed TB research”

    An Open Source Integrated Computational Resource for the Analysis of the Structural Interactome to predict Off-Site Interactions of Drug Candidates

    Nagasuma Chandra, R. Sowdhamini, N. Srinivasan & Sir Tom Blundell


    Ongoing cheminformatics
    Ongoing: Cheminformatics bypassed TB research”

    Community of About 400

    PubChem

    ChEMBL

    DrugBank

    HT Virtual screening

    Cheminformatics Models

    Experimental Assays

    Curated molecule datasets

    Data Mining and Analysis

    • Other Active Communities:

      • OSDD Women Scientists Forum

      • OSDD Junior Scientists Forum


    Cheminformatics bypassed TB research” – Large Scale Data Analysis

    Data

    Processing

    Size increases

    Heap Size issues

    Software

    Power MV and WEKA

    Output


    Cheminformatics large scale data analysis
    Cheminformatics – Large Scale Data Analysis bypassed TB research”

    • Accessing large data files from online repository such as Pub Chem.

    • Basic computational resources – 4Gb RAM

    Pub Chem

    Database

    1.04Pb

    Max bandwidth - 1-4 Mbps

    Local Systems

    4Gb RAM


    C dac s garuda grid indian grid computing initiative
    C-DAC’s Garuda Grid – bypassed TB research” Indian Grid Computing Initiative

    • C-DAC is R&D organization under Ministry of Communication & Information Technology, India

    • C-DAC’s Garuda Grid is targeted at providing a facility for the scientific community, which would enable them to seamlessly access the distributed resources.

    • Compute Power of GARUDA: ~ 70TFs (6000 CPUs)

    • Currently there are 55 Garuda Partners

    • Has NKN (National Knowledge Network) connectivity at 10Gbps


    Garuda usage by osdd job accounting
    Garuda Usage by OSDD: bypassed TB research”Job Accounting


    OSDD - Linking Institutions and Competencies bypassed TB research”

    45 Hits Selected for Screening

    Hits identified through virtual screening are synthesized and tested for enzyme assay


    Creation of Library of Drug Like Compounds bypassed TB research”

    Filtering Criteria for Pruning 50,000 compounds

    from Chembridge Database

    • Molecular Weight < 400

    • Remove molecules other than H,C,N,O,F,S,P,Cl,Br, or I

    • ADME properties (Principle descriptors & Prediction of properties) based on 1712 drugs.

    • Shrinking the CLogP window between 1.5 & 5

    A physical compound library of drug like compounds. (20,000 compounds)

    Whole cell screening


    Osdd open chemistry
    OSDD Open Chemistry bypassed TB research”

    Led by CSIR- CDRI, India’s National Drug Research Laboratory


    Osdd open chemistry1
    OSDD Open Chemistry bypassed TB research”

    • Challenge

      Need novel molecules for screening against TB/Malaria

    • OSDD Approach

    • Open source small molecule synthesis involving 40 chemistry departments from colleges across India

    • Web based collaboration and discussion


    OSDD Team at work in SASTRA bypassed TB research”

    Project implementation through students selected via pan India online primer designing exercise

    More than 30 genes cloned in less than 3 months


    POC for downstream experiments bypassed TB research”

    • Fifteen undergraduate students were given hands on training in various Molecular biology techniques

    • So far, 11 genes have been cloned in pGEM-T easy vector

    • 20 have been cloned in pET28 a/b/c and expressed (Verified by SDS –PAGE)


    Status bypassed TB research”: OSDD Projects

    18

    Other projects aim to develop tools, databases and repositories for the OSDD community

    19

    9

    6

    2


    OSDD Publications bypassed TB research”

    • Bhardwaj A, et al. Open Source Drug Discovery- a new paradigm of collaborative research in Tuberculosis drug development. Tuberculosis, 2011 (in press)

    • Bhardwaj A, et al. Collaborative Tools to Accelerate Neglected Disease Research: the Open Source Drug Discovery Model [Book Chapter]in Collaborative Computational Technologies for Biomedical Research, Wiley and Sons, May 2011.

    • Bhat AG, et al. Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with Isoniazid. Systems and Synthetic Biology. 2011 Volume 4, Number 4, 299-309.

    • Sharma S, et al. Piperine as an inhibitor of Rv1258c, a putative multidrug efflux pump of Mycobacterium tuberculosis. J AntimicrobChemother. 2010 Aug;65(8):1694-701.

    • Mishra NK, et al. Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule. BMC Pharmacol. 2010 Jul 16; 10:8.

    • Mathew R, et al. Inhibition of mycobacterial growth by plumbagin derivatives. ChemBiol Drug Des. 2010 Jul 76(1); 34-42.

    • Garg A, et al. KiDoQ: using docking based energy scores to developligand based model for predicting antibacterials. BMC Bioinformatics. 2010 Mar 11;11:125.

    • Bhardwaj A, et al. Open Source Drug Discovery Consortium, TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2009 Sep; 89(5):386-7.

    • Bhardwaj A, et al . Open source drug discovery: a global collaborative drug discovery model for tuberculosis. Science and culture, January-February, 2011, vol. 77, nos. 1–2, 22-26.


    Geek Nation: How Indian Science Is Taking Over The World bypassed TB research”

    “..a journey to meet the inventors, engineers and young scientists behind this nation built not on conquest, oil or minerals, but on the scientific ingenuity of its people..”

    “.. explores the reason why the government of the most religious country on earth has put its faith in science and technology..”

    “..The West may think India is still in the gutter, but it is looking at the stars..”

    Author, Angela Saini


    Responses from the OSDD Community bypassed TB research”

    • I have had a thrilling experience with OSDD for the past 2 years and now I am ready to pursue my PHD at Indiana University

    • Abhik Seal, SBI Employee, Calcutta

    • I can access the CDAC supercomputing facility The Garuda Grid sitting at any place from anywhere in the world.

    • Rajdeep Poddar, Bio IT Application Specialist

    • OSDD is a boon to me, giving me a platform to research when I was at cross roads regarding career ,family and research

    • Swati Gandhi ,Baroda, Gujrat

    • It has been a dream come true and a great learning experience after becoming a part of OSDD

    • Dr Preetha Anil, SIAS, Kerala

    • I still remember what I said to myself on second day of OSDD conference looking into the mirror... “Is this the Shamsudheen from that remote village?????....!!!!!”

    • Shamsudheen K.V ,IGIB


    • Together bypassed TB research” we can …

    • .. and weshould !

    http://www.osdd.net

    http://c2d.osdd.net

    http://sysborg2.osdd.net

    Matt Smadley | Flickr.com


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