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Overview of Chemical Informatics and Cyberinfrastructure Collaboratory

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Chemical Informatics Cyberinfrastructure/Grids with services, workflows and ... Barnard (Digital Chemistry) John Reynders (Eli Lilly) ... – PowerPoint PPT presentation

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Title: Overview of Chemical Informatics and Cyberinfrastructure Collaboratory


1
Overview of Chemical Informatics and
Cyberinfrastructure Collaboratory
  • Aug 16 2006
  • Geoffrey Fox
  • Computer Science, Informatics, Physics
  • Pervasive Technology Laboratories
  • Indiana University Bloomington IN 47401
  • gcf_at_indiana.edu
  • http//www.infomall.org
  • http//www.chembiogrid.org

2
Capabilities
  • Local Teams, successful Prototypes and
    International Collaboration set up in 3 initial
    major focus areas
  • Chemical Informatics Cyberinfrastructure/Grids
    with services, workflows and demonstration uses
    building on success in other applications (LEAD)
    and showing distributed integration of academic
    and commercial tools
  • Computational Chemistry Cyberinfrastructure/Grids
    with simulation, databases and TeraGrid use
  • Education with courses and degrees
  • Review of activities suggest we also formalize
    work in two further areas
  • Chemical Informatics Research model
    applicability
  • Interfacing with the User - bench
    chemist-friendly portal

3
Current Status
  • Web site http//www.chembiogrid.org
  • Wiki chosen to support project as a shared
    editable web space
  • Building Collaboratory involving PubChem Global
    Information System accessible anywhere and at any
    time enhance PubChem with distributed tools
    (clustering, simulation, annotation etc.) and
    data
  • Adopted Taverna as workflow as popular in
    Bioinformatics but we will evaluate other systems
    such as GPEL from LEAD
  • Preparing large set of runs on local Big Red 23
    Teraflop supercomputer (OSCAR3 CDK Mopac)
  • Initial results discussed at conferences/workshops
    /papers
  • Gordon Conferences, ACS, SDSC tutorial
  • First new Cheminformatics courses offered
  • Advisory board set up and met
  • Videoconferencing-based meetings with Peter
    Murray-Rust and group at Cambridge roughly every
    2-3 weeks
  • Good or potentially good interactions with NIH
    DTP, Scripps, Lilly and Michigan ECCR

4
CICC Senior Personnel
  • Peter T. Cherbas
  • Mehmet M. Dalkilic
  • Charles H. Davis
  • A. Keith Dunker
  • Kelsey M. Forsythe
  • Kevin E. Gilbert
  • John C. Huffman
  • Malika Mahoui
  • Daniel J. Mindiola
  • Santiago D. Schnell
  • William Scott
  • Craig A. Stewart
  • David R. Williams
  • Geoffrey C. Fox
  • Mu-Hyun (Mookie) Baik
  • Dennis B. Gannon
  • Marlon Pierce
  • Beth A. Plale
  • Gary D. Wiggins
  • David J. Wild
  • Yuqing (Melanie) Wu

From Biology, Chemistry, Computer Science,
Informatics at IU Bloomington and IUPUI
(Indianapolis)
5
CICC Advisory Board
  • Alan D. Palkowitz (Eli Lilly)
  • Chris Peterson (Kalypsys)
  • David Spellmeyer (IBM)
  • Dimitris K. Agrafiotis (Johnson Johnson)
  • Horst Hemmerle (Eli Lilly)
  • James M. Caruthers (Purdue University)
  • Jeremy G. Frey (University of Southampton)
  • Joel Saltz (Ohio State University/University of
    Maryland/Johns Hopkins University)
  • John M. Barnard (Digital Chemistry)
  • John Reynders (Eli Lilly)
  • Peter Murray-Rust (University of Cambridge)
  • Peter Willett (University of Sheffield)
  • Thompson Doman (Eli Lilly)
  • Val Gillet (University of Sheffield)

Industry andAcademia Met October 2005 will meet
this fall
6
Chemical Informatics and Cyberinfrastucture
Collaboratory Funded by the National Institutes
of Health www.chembiogrid.org
CICC
CICC
CICC Combines Grid Computing with Chemical
Informatics
Large Scale Computing Challenges
Science and Cyberinfrastructure
CICC is an NIH funded project to support chemical
informatics needs of High Throughput Cancer
Screening Centers. The NIH is creating a data
deluge of publicly available data on potential
new drugs.
Chemical Informatics is non-traditional area of
high performance computing, but many new,
challenging problems may be investigated.
NIH PubMed DataBase
OSCAR Text Analysis
Toxicity Filtering
Cluster Grouping
Docking
.
Initial 3D Structure Calculation
OSCAR-mined molecular signatures can be
clustered, filtered for toxicity, and docked onto
larger proteins. These are classic pleasingly
parallel tasks. Top-ranking docked molecules
can be further examined for drug potential.
Chemical informatics text analysis programs can
process 100,000s of abstracts of online
journal articles to extract chemical signatures
of potential drugs.
Molecular Mechanics Calculations
Big Red (and the TeraGrid) will also enable us to
perform time consuming, multi-stepped Quantum
Chemistry calculations on all of PubMed. Results
go back to public databases that are freely
accessible by the scientific community.
  • CICC supports the NIH mission by combining state
    of the art chemical informatics techniques with
  • World class high performance computing
  • National-scale computing resources (TeraGrid)
  • Internet-standard web services
  • International activities for service
    orchestration
  • Open distributed computing infrastructure for
    scientists world wide

NIH PubChem DataBase
Quantum Mechanics Calculations
IUs Varuna DataBase
POVRay Parallel Rendering
Indiana University Department of Chemistry,
School of Informatics, and Pervasive Technology
Laboratories
7
CICC Prototype Web Services
Basic cheminformatics
Key Ideas
Molecular weights Molecular formulae Tanimoto
similarity 2D Structure diagrams Molecular
descriptors 3D structures InChi
generation/search CMLRSS
  • Add value to PubChem with additional distributed
    services and databases
  • Wrapping existing code in web services is not
    difficult
  • Provide core (CDK) services and exemplars of
    typical tools
  • Provide access to key databases via a web
    service interface
  • Provide access to major Compute Grids

Application based services
Compare (NIH) Toxicity predictions
(ToxTree) Literature extraction
(OSCAR3) Clustering (BCI Toolkit) Docking,
filtering, ... (OpenEye)Varuna simulation
8
Varuna environment for molecular modeling (Baik,
IU)
Researcher
Chemical Concepts
Papers etc.
Experiments
ChemBioGrid
Simulation ServiceFORTRAN Code, Scripts
DB ServiceQueries, Clustering,Curation, etc.
QM Database
ReactionDB
Condor
PubChem, PDB,NCI, etc.
QM/MM Database
TeraGridSupercomputersFlocks
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