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MIBLab Workshop E-Cell Project

29 June, 2006. MIBLab Workshop E-Cell Project. E-Cell. www.e-cell.org Model and reconstruct biological phenomena In silico Precise whole cell simulation. Organization. Headquarters - Institute for Advanced Biosciences, Keio University

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MIBLab Workshop E-Cell Project

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  1. 29 June, 2006 MIBLab WorkshopE-Cell Project

  2. E-Cell • www.e-cell.org • Model and reconstruct biological phenomena • In silico • Precise whole cell simulation

  3. Organization • Headquarters - Institute for Advanced Biosciences, Keio University • Original Home – Shonan-Fujisawa Campus, Keio University • The Molecular Sciences Institute, Berkeley • Mitsubishi Space Software Co. Ltd., Amagasaki

  4. History • Project Launch – 1996 • Cell model with 127 genes – 1997 • Modeling real cells – 1998 • The Institute for Advanced Biosciences – 2001

  5. Research Focuses • Modeling methodologies • E-Cell system • Numerical simulation algorithms • Mathematical analysis methods

  6. Research Group • Mitochondrion • E-Neuron • E2coli • e-Rice • Erythrocyte • Cell signaling • Bacterial chemotaxis signaling pathway • Stoch Sim algorithm • Circadian rhythm, diabetes, mathematical analysis, myocardial cell

  7. E-Cell Parts • E-Cell Simulation Environment (E-Cell SE) • E-Cell Modeling Environment (E-Cell ME) • E-Cell Analysis Toolkit

  8. System Features • Object-oriented modeling and simulation • Plug-in architecture • Real-time user interaction and visualization

  9. Simulation Algorithms • Gillespie • Ordinary differential equations • Differential-algebraic equations • Power-law formalisms • Flux distribution / discrete-time simulator

  10. Scripting • Simulation session • Analysis session • Model file generation

  11. SBML / Parallel computation • SBML level 1/2 import / export • Parallel stepper scheduling (under development) • Distributed computing

  12. Platforms • Fedora core 3 • Windows XP / 2000 (beta) • RedHat Enterprise Linux on IBM pSeries • Mandrake Linux 10 • Future platforms • IBM AIX • Linux / x86-64 • Linux / IA64

  13. Tutorial • Online tutorial (E-Cell Wiki) • http://www.e-cell.org/community/tutorials • ICSB 2006, Yokohama

  14. Simple Pathway • Substrate (S) • Enzyme (E) • Product (P)

  15. Select Trace and Run

  16. Change Concentration and Run

  17. Modeling with E-Cell • Entity (more than one) • Variable • Process • system • Stepper

  18. EM Example

  19. Testing Result • Pathway modeling tool • A lot of numerical solvers • XML model (EML) • Cannot run other tools

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