Difference between revisions of "Simulation"
Ilya Kiselev (Talk | contribs) |
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| + | Simulation engine is a tool used for transformation visual diagram into numerical model and performing simulation. Each simulation engine is applicable to certain types of diagrams. | ||
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Currently, BioUMl contains next simulation engines: | Currently, BioUMl contains next simulation engines: | ||
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*Agent-based Simulation Engine | *Agent-based Simulation Engine | ||
*Hemodynamics Simulation Engine | *Hemodynamics Simulation Engine | ||
| + | *FBA Simulation Engine | ||
== ODE Simulation Engine == | == ODE Simulation Engine == | ||
| − | Generates ODE system with descrete events. Along with the initial model state it constitutes Initial Value Problem (IVP) which can be solved with appropriate methods implemented in BioUML: | + | Generates ODE system with descrete [[events]]. Along with the initial model state it constitutes Initial Value Problem (IVP) which can be solved with appropriate methods implemented in BioUML: |
*[[Euler]] | *[[Euler]] | ||
*[[Dormand-Prince]] | *[[Dormand-Prince]] | ||
*[[RADAU V]] | *[[RADAU V]] | ||
*[[JVODE]] | *[[JVODE]] | ||
| + | *[[Imex]] | ||
It is also applicable for [[modular modeling|modular models]] created in BioUML and satisfying certain limitations on modules. In that case [[flattening algorithm]] is applied before simulation. | It is also applicable for [[modular modeling|modular models]] created in BioUML and satisfying certain limitations on modules. In that case [[flattening algorithm]] is applied before simulation. | ||
Revision as of 12:48, 10 February 2017
Simulation engine is a tool used for transformation visual diagram into numerical model and performing simulation. Each simulation engine is applicable to certain types of diagrams.
Currently, BioUMl contains next simulation engines:
- ODE Simulation Engine
- Stochastic Simulation Engine
- Agent-based Simulation Engine
- Hemodynamics Simulation Engine
- FBA Simulation Engine
Contents |
ODE Simulation Engine
Generates ODE system with descrete events. Along with the initial model state it constitutes Initial Value Problem (IVP) which can be solved with appropriate methods implemented in BioUML:
It is also applicable for modular models created in BioUML and satisfying certain limitations on modules. In that case flattening algorithm is applied before simulation.
Stochastic Simulation Engine
Interpretes chemical reactions in the model as stochastic processes. Generated code implements interface for stochastic solvers:
Agent-based Simulation Engine
Is applicable for modular models regardless modules implementation. Each module is simulated with its own simulation engine, scheduler provides their intercommunications.
Hemodynamics Simulation Engine
Serves for simulation of the blood flow across arterial tree. Provides mathematical model generation on the basis of visually represented arterial tree and its simulation. Mathematical model is a set of PDE (partial differential equations).
