Difference between revisions of "Simulation"

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(ODE Simulation Engine)
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Allowed diagram types:
 
Allowed diagram types:
 +
*[[Pathway simulation]]
 +
*[[Composite model]]
 +
*[[SBML model in SBGN notation]]
 +
*[[SBML "comp" model in SBGN nptation]]
 +
 +
For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation.
  
 
Available simulators:
 
Available simulators:
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*[[JVODE]]
 
*[[JVODE]]
 
*[[Imex]]
 
*[[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.
 
  
 
== Stochastic Simulation Engine ==
 
== Stochastic Simulation Engine ==

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).

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