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Research Cyberinfrastructure: Biological/Life Sciences

Research Cyberinfrastructure: Biological/Life Sciences. Frank Doyle Institute for Collaborative Biotechnologies UC, Santa Barbara. Major Research Centers. $50M Institute for Collaborative Biotechnologies (ARO/ARL) $8.4M Center for Bio-Image Informatics (NSF)

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Research Cyberinfrastructure: Biological/Life Sciences

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  1. Research Cyberinfrastructure:Biological/Life Sciences Frank Doyle Institute for Collaborative Biotechnologies UC, Santa Barbara

  2. Major Research Centers • $50M Institute for Collaborative Biotechnologies (ARO/ARL) • $8.4M Center for Bio-Image Informatics (NSF) • $100M California Nanosystems Institute (CISI)

  3. Nature of Our Research • Systems Biology • Complex multi-scale, stochastic simulation of biophysical networks (10,000s of nodes, each with 10s-100s of equations) • Robustness & sensitivity analysis • Global optimization & experimental design • Bio-Image Informatics • Massive amounts of image and video data (storage, distribution, access, visualization) • Many others • Stochastic Simulation for Biomembrane Dynamics • Bioinformatics: Querying and Mining Databases • Simulations of Protein Folding and Aggregation • Field Theoretic Computer Simulations of Complex Fluids/Biosensors

  4. Example: Gene Organism Models for Circadian Rhythm Organs (~10,000 cells) Gene Networks (~100 stochastic ODEs) Organism [Forger & Peskin, 2003] [Reppert & Weaver, 2002]

  5. Major Information Technology Thrusts in Bio-Imaging

  6. Systems Biology Software Tool Development Stochastic Simulation Sensitivity Analysis

  7. Critical Dependencies on Cyberinfrastructure • Facilities • Space, power & cooling (often met by ORUs) • Networking • HPCC Systems Support • Hardware & software • HPCC Users Support • Application development • Parallel code optimization • Data Support • support for large- scale, heterogeneous, & distributed scientific databases • Software infrastructure for system integration

  8. Research Limitations due to (lack of) Cyberinfrastructure • Complexity and scale of models for simulation • Inherently local as opposed to global analysis • Resolution of imaging • Dimensions of databases • Data assimilation • Portability support

  9. Specific Recommendations • Campus CI Technical  Support • Requires funding and organizational support • Support (UC) cross-campus initiatives (e.g., CNSI) • Support broader collaborative initiatives (DOE labs, other campuses) • Better network connectivity

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