MIBLab Workshop E-Cell Project 29 June, 2006

E-Cell 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) 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