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Research Cyberinfrastructure: Biological/Life Sciences

The Institute for Collaborative Biotechnologies at UC Santa Barbara, supported by over $150M in funding, focuses on research in systems biology and complex multi-scale simulations. Key projects involve stochastic simulations for biomembrane dynamics, bioimage informatics, and protein folding, leveraging extensive cyberinfrastructure to enable high-performance computing and data analysis. By addressing critical dependencies and limitations in current cyberinfrastructure, the institute aims to enhance collaborative research across biology and technology, facilitating breakthroughs in understanding complex biological systems.

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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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