Simulation - Revision history

Axec@dote.ru at 15:25, 12 February 2017

2017-02-12T15:25:26Z

2017-02-12T15:00:54Z

2017-02-12T15:00:20Z

‎ODE Simulation Engine

2017-02-12T14:52:30Z

2017-02-10T05:49:41Z

2017-02-10T05:48:44Z

2015-11-11T06:52:30Z

2013-08-01T14:28:05Z

2013-06-04T04:14:23Z

Link fixed - ‎ODE Simulation Engine

2013-06-04T04:13:26Z

Link fixed - ‎Agent-based Simualtion Engine

@@ Line 8: / Line 8: @@
 *Hemodynamics Simulation Engine
 *FBA Simulation Engine
 == ODE Simulation Engine ==
@@ Line 18: / Line 25: @@
 *[[SBML "comp" model in SBGN notation]]
-For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation.
+For composite (and SBML "comp") diagrams special "flattening" algorithm is performed before the simulation.
 Available simulators:
@@ Line 28: / Line 35: @@
 == Stochastic Simulation Engine ==
-Interpretes chemical reactions in the model as stochastic processes. Generated code implements interface for stochastic solvers:
+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.
 *[[Simple Gillespie]]
 *[[Gibson-Bruck]]

@@ Line 1: / Line 1: @@
 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:
+Currently, BioUML contains next simulation engines:
 *ODE Simulation Engine
@@ Line 16: / Line 16: @@
 *[[Composite model]]
 *[[SBML model in SBGN notation]]
-*[[SBML "comp" model in SBGN nptation]]
+*[[SBML "comp" model in SBGN notation]]
 For composite models (and SBML "comp") models special "flattening" algorithm is performed before the simulation.

@@ Line 13: / Line 13: @@
 Allowed diagram types:
 Available simulators:
@@ Line 20: / Line 26: @@
 *[[JVODE]]
 *[[Imex]]
 == Stochastic Simulation Engine ==

@@ Line 1: / Line 1: @@
-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.
+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:
@@ Line 10: / Line 10: @@
 == 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:
+Engine works with ODE (Ordinary Differential Equations) models which additionally may contain algebraic equations and [[descrete events]].
 *[[Euler]]
 *[[Dormand-Prince]]

@@ Line 10: / Line 10: @@
 == 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]]
 *[[Dormand-Prince]]

@@ Line 4: / Line 4: @@
 *Stochastic Simulation Engine
 *Agent-based Simulation Engine
 == ODE Simulation Engine ==
@@ Line 21: / Line 22: @@
 *[[Maximum time-step]]
-== Agent-based Simualtion Engine ==
+== Agent-based Simulation Engine ==
 Is applicable for [[modular modeling|modular models]] regardless modules implementation. Each module is simulated with its own simulation engine, scheduler provides their intercommunications.

@@ Line 12: / Line 12: @@
 *[[JVODE]]
-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.
+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 ==

← Older revision		Revision as of 04:13, 4 June 2013
Line 22:		Line 22:

	== Agent-based Simualtion Engine ==		== Agent-based Simualtion 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.