miblab workshop e-cell project 29 june, 2006. e-cell model and reconstruct biological phenomena in...
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MIBLab WorkshopE-Cell Project
29 June, 2006
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
• Original Home – Shonan-Fujisawa Campus, Keio University
• The Molecular Sciences Institute, Berkeley• Mitsubishi Space Software Co. Ltd.,
Amagasaki
History
• Project Launch – 1996• Cell model with 127 genes – 1997• Modeling real cells – 1998• The Institute for Advanced Biosciences –
2001
Research Focuses
• Modeling methodologies• E-Cell system• Numerical simulation algorithms• Mathematical analysis methods
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
E-Cell Parts
• E-Cell Simulation Environment (E-Cell SE)• E-Cell Modeling Environment (E-Cell ME)• E-Cell Analysis Toolkit
System Features
• Object-oriented modeling and simulation• Plug-in architecture• Real-time user interaction and
visualization
Simulation Algorithms
• Gillespie• Ordinary differential equations• Differential-algebraic equations• Power-law formalisms• Flux distribution / discrete-time simulator
Scripting
• Simulation session• Analysis session• Model file generation
SBML / Parallel computation
• SBML level 1/2 import / export• Parallel stepper scheduling (under
development)• Distributed computing
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
Tutorial
• Online tutorial (E-Cell Wiki)• http://www.e-cell.org/community/tutorials• ICSB 2006, Yokohama
Simple Pathway
• Substrate (S)• Enzyme (E)• Product (P)
Select Trace and Run
Change Concentration and Run
Modeling with E-Cell
• Entity (more than one)– Variable– Process– system
• Stepper
EM Example
Testing Result
• Pathway modeling tool• A lot of numerical solvers• XML model (EML)• Cannot run other tools
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