Difference between revisions of "Simulation"
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
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| − | Currently, | + | 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 | *ODE Simulation Engine | ||
*Stochastic Simulation Engine | *Stochastic Simulation Engine | ||
*Agent-based Simulation Engine | *Agent-based Simulation Engine | ||
| + | *Hemodynamics Simulation Engine | ||
| + | *FBA Simulation Engine | ||
| + | |||
| + | All engines have common options: | ||
| + | *''Initial time'' - initial value of time variable. It is strongly recommended to use only 0 value here. | ||
| + | *''Time increment'' - gap between time points at which results of the simulation will be recordered. | ||
| + | *''Completion time'' - time point at which simulation will end. | ||
| + | *''Simulator name'' - choosen numerical simulator. | ||
| + | *''Simulator options'' - options of chosen simulator. | ||
== ODE Simulation Engine == | == ODE Simulation Engine == | ||
| − | + | Engine works with ODE (Ordinary Differential Equations) models which additionally may contain algebraic equations and [[descrete events]]. | |
| + | |||
| + | Allowed diagram types: | ||
| + | *[[Pathway simulation]] | ||
| + | *[[Composite model]] | ||
| + | *[[SBML model in SBGN notation]] | ||
| + | *[[SBML "comp" model in SBGN notation]] | ||
| + | |||
| + | For composite (and SBML "comp") diagrams special "flattening" algorithm is performed before the simulation. | ||
| + | |||
| + | Available simulators: | ||
*[[Euler]] | *[[Euler]] | ||
*[[Dormand-Prince]] | *[[Dormand-Prince]] | ||
| − | *[[RADAU | + | *[[RADAU V]] |
*[[JVODE]] | *[[JVODE]] | ||
| − | + | *[[Imex]] | |
| − | + | ||
== Stochastic Simulation Engine == | == Stochastic Simulation Engine == | ||
| − | + | Engine works with stochastic (Gillespie-type) models which additionally may contain [[descrete events]]. It is applicable to diagrams with net of reactions. Reactions are interpreted as stochastic processes. | |
| + | |||
| + | Allowed diagram types: | ||
| + | *[[Pathway simulation]] | ||
| + | *[[Composite model]] | ||
| + | *[[SBML model in SBGN notation]] | ||
| + | *[[SBML "comp" model in SBGN notation]] | ||
| + | |||
| + | It ignores all equations (scalar, algebraic and differential) in such diagrams. For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation. | ||
| + | |||
*[[Simple Gillespie]] | *[[Simple Gillespie]] | ||
*[[Gibson-Bruck]] | *[[Gibson-Bruck]] | ||
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*[[Maximum time-step]] | *[[Maximum time-step]] | ||
| − | == Agent-based | + | == 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. | + | Is applicable for [[modular modeling|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). | ||
Latest revision as of 22:25, 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
All engines have common options:
- Initial time - initial value of time variable. It is strongly recommended to use only 0 value here.
- Time increment - gap between time points at which results of the simulation will be recordered.
- Completion time - time point at which simulation will end.
- Simulator name - choosen numerical simulator.
- Simulator options - options of chosen simulator.
Contents |
[edit] 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 (and SBML "comp") diagrams special "flattening" algorithm is performed before the simulation.
Available simulators:
[edit] Stochastic Simulation Engine
Engine works with stochastic (Gillespie-type) models which additionally may contain descrete events. It is applicable to diagrams with net of reactions. Reactions are interpreted as stochastic processes.
Allowed diagram types:
It ignores all equations (scalar, algebraic and differential) in such diagrams. For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation.
[edit] 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.
[edit] 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).
