Cell Electrophysiology Simulation Environment CESE

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Cell Electrophysiology Simulation Environment
(CESE)

• 29 June, 2006

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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

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Users

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

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Features

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

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Developers

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

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Model Creation

• What you need
• J2SDK
• Java IDE
• CESE source
• Extending model
• Creating model
• Data exporter

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Example

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

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Hodgkin-Huxley Equation
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Extending Model

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

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Create New Model

• Override doSimulate() method
• JavaBeans specification
• Private
• Read-only

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Export Data

• public abstract void prepareExport()
• public abstract void doExport(int count)
• public abstract void finishExport()

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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