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