MIBLab Workshop E-Cell Project

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MIBLab WorkshopE-Cell Project

• 29 June, 2006

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E-Cell

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

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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

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History

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

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Research Focuses

• Modeling methodologies
• E-Cell system
• Numerical simulation algorithms
• Mathematical analysis methods

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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

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E-Cell Parts

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

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System Features

• Object-oriented modeling and simulation
• Plug-in architecture
• Real-time user interaction and visualization

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Simulation Algorithms

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

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Scripting

• Simulation session
• Analysis session
• Model file generation

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SBML / Parallel computation

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

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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

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Tutorial

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

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Simple Pathway

• Substrate (S)
• Enzyme (E)
• Product (P)

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Select Trace and Run
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Change Concentration and Run
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Modeling with E-Cell

• Entity (more than one)
• Variable
• Process
• system
• Stepper

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EM Example
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Testing Result

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