Difference between revisions of "Simulation"
Ilya Kiselev (Talk | contribs) (→ODE Simulation Engine) |
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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 and defines set of numerical simulators suitable for these diagrams. | 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 and defines set of numerical simulators suitable for these diagrams. | ||
| − | Currently, | + | Currently, BioUML contains next simulation engines: |
*ODE Simulation Engine | *ODE Simulation Engine | ||
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*[[Composite model]] | *[[Composite model]] | ||
*[[SBML model in SBGN notation]] | *[[SBML model in SBGN notation]] | ||
| − | *[[SBML "comp" model in SBGN | + | *[[SBML "comp" model in SBGN notation]] |
For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation. | For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation. | ||
Revision as of 22:00, 12 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 and defines set of numerical simulators suitable for these 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
Engine works with ODE (Ordinary Differential Equations) models which additionally may contain algebraic equations and descrete events.
Allowed diagram types:
For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation.
Available simulators:
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).
