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BioSPICE and Problem-Solving Environments for Systems Biology Clifford A. Shaffer Department of Computer Science Virgini

BioSPICE and Problem-Solving Environments for Systems Biology Clifford A. Shaffer Department of Computer Science Virginia Tech. Systems Biology. Focus on regulatory mechanisms for biochemical networks Start with a wiring diagram Some example problems: Cell Cycle Circadian Rhythms.

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BioSPICE and Problem-Solving Environments for Systems Biology Clifford A. Shaffer Department of Computer Science Virgini

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  1. BioSPICE and Problem-Solving Environments for Systems BiologyClifford A. ShafferDepartment of Computer ScienceVirginia Tech

  2. Systems Biology • Focus on regulatory mechanisms for biochemical networks • Start with a wiring diagram • Some example problems: • Cell Cycle • Circadian Rhythms

  3. Sister chromatid separation Unaligned Xsomes Cdh1 Clb5 Clb2 Cdc20 Cdc20 Mcm1 Clb2 Sic1 Mitosis Clb2 Clb2 Cdc20 Sic1 Sic1 Swi5 P Sic1 Cln2 Clb5 Clb? Budding Cln2 SBF Mass Cdh1 Cln3 and Bck2 SCF Cdc20 MBF Clb5 DNA synthesis

  4. synthesis synthesis binding degradation degradation activation inactivation

  5. G1 S/M Simulation of the budding yeast cell cycle mass Sic1 Cln2 Clb2 Cdh1 Cdc20 Time (min)

  6. Experimental Databases Usage Scenario Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparator Data Notebook

  7. The Cell (Modeler) Cycle • Outer Loop: • Define Reaction Equations • Inner Loop: • Adjust parameters, initial conditions

  8. Fundamental Activities • Collect information • Search literature (databases), Lab notebooks • Define/modify models • A user interface problem • Run simulations • Equation solvers (ODEs, PDEs, deterministic, stochastic) • Compare simulation results to experimental data • Analysis

  9. Our Mission: Build Software to Help the Modelers • Now: Typical cycle time for changing the model is one month • Collect data on paper lab notebooks • Convert to differential equations by hand • Calibrate the model by trial and error • Inadequate analysis tools • Goal: Change the model once per day. • Bottleneck should shift to the experimentalists

  10. Tools • Specifications for defining models (markup languages) • “Electronic Lab Notebooks” and access to literature, experiments, etc. • User interface for specifying models, parameters, initial conditions • Automated parameter estimation (calibration) • Analysis tools for comparing simulation results and experimental results • Database support for simulations (data mining)

  11. BioSPICE • DARPA project • Approximately 15 groups • Many (not all) of the systems biology modelers and software developers • An explicit integration team • Goal: Define mechanisms for interoperability of software tools, build an expandable problem solving environment for systems biology • Result: software tools contributed by the community to the community

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