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Class Summary |
| AsynchronousCultureRunner |
Computes the average concentration levels in an asynchronous culture. |
| CPPExpression |
This code is licensed under the DARPA BioCOMP Open Source License. |
| EnsembleLauncher |
Runs StochKit on an SBML file multiple times to collect ensemble result. |
| EnsembleSimulator |
Makes the StochKit simulator available to the simulator API. |
| Oscill8Launcher |
Runs Oscill8 on an SBML file. |
| Oscill8Simulator |
Makes the Oscill8 simulator available to the simulator API. |
| SBMLToStochKitTranslator |
Translate SBML file produced from JigCell into C++ file as input of Stochkit
feature history:
supports algebaric rule, and assignment rule
- mediate variable assignment (seems useless and causes error)
* support for pow
+ support for function
* support for safe name check
+ support for events
* adjust rules
* clean up the code
* assign event number by calculating power in vivo v1.4
* make name c++ safe by edit SymbolTable.makeFortranSafe
* special treatment for Vn, should be changed later v1.5
+ execute stochkit
+ add "double t" to eventAction method v1.6
* LOG and SQRT to log and sqrt
* eliminate NaN in parameter declaration. |
| SBMLToXPPTranslator |
Translates an SBML model to ODEs. |
| StochKitLauncher |
Runs StochKit on an SBML file. |
| StochKitSimulator |
Makes the StochKit simulator available to the simulator API. |
| Stopwatch |
A class to help benchmark code
It simulates a real stop watch |
| StreamGobbler |
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| SymbolTable |
Caution: This code has been modified by Pengyuan to be used for CPP code. |
| SymbolTable.Mode |
These constants describe the type of symbol table. |
| XPPLauncher |
Runs XPP on an SBML file. |
| XPPSimulator |
Makes the XPP simulator available to the simulator API. |