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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
– Hodgkin-Huxley
– Markovian current formulations
• Electrical activity
• Future neuronal model
Features
•
•
•
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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:
– 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
– 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