Cell Electrophysiology Simulation Environment (CESE) 29 June, 2006

CESE Computational electrophysiological simulations action potentials individual ionic currents changes in ionic concentrations Cross-platform (JRE 1.4 or above) Windows, Linux, Solaris, MacOS X, AIX

Users Single-cell model Electrical activity Future neuronal model Hodgkin-Huxley Markovian current formulations Electrical activity Future neuronal model

Features Uniform interface Voltage clamp for complex model behavior Data visualization Current-voltage plots and statistical parameter calculation Export to ASCII, ATF, NetCDF CellML

Developers Java API Implementation of house-keeping routines Models conform to JavaBeans specification XML clamping commands Java object serialization Open-source

Model Creation What you need: Extending model Creating model J2SDK Java IDE CESE source Extending model Creating model Data exporter

Example Luo-Rudy Mammalian Ventricular Model I, 1991 Simulate guinea pig ventricular action potentials

Hodgkin-Huxley Equation

Extending Model Replacement Object oriented programming modify source code change BeanInfo class recompile package Object oriented programming extend class Override BeanInfo class recompile

Create New Model Override doSimulate() method JavaBeans specification Private Read-only

Export Data public abstract void prepareExport() public abstract void doExport(int count) public abstract void finishExport()

Is It Useful? Fancy plotter Any model that is similar to that in our case? Simple stepper Limited functions Hodgkin-Huxley and Markovian can be “mixed” Only one Markovian current formulations