Simulation

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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.

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

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:

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.

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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