Parameter fitting (analysis) - Revision history

WikiBot: Automatic synchronization with BioUML

2020-12-09T11:15:20Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2019-03-12T09:32:38Z

Automatic synchronization with BioUML

WikiBot: Protected "Parameter fitting (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

2017-02-13T12:00:39Z

Protected "Parameter fitting (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2017-02-13T12:00:32Z

Automatic synchronization with BioUML

New page

;Analysis title
:[[File:DAE-models-Parameter-fitting-icon.png]] Parameter fitting
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.optimization.analysis.ParameterFitting}}
;Plugin
:[[Biouml.plugins.optimization (plugin)|biouml.plugins.optimization (Optimization plug-in)]]

==== Parameters: ====

* '''Input diagram''' – Input diagram
* '''Experiment table''' – Experiment table
* '''Algorithm''' – Algorithm
** '''type''' – type
** '''Iterations number''' – Iterations number
** '''Survival size''' – Survival size
* '''Parameters group''' – Parameters group
** '''Parameters''' – Parameters
* '''Result''' – Result
* '''Simulation engine''' – Simulation engine
** '''Engine type''' – Engine type.
** '''Engine options''' – Engine options.
*** '''Initial time''' – Initial time.
*** '''Completion time''' – Completion time.
*** '''Time increment''' – Time increment.
*** '''Simulator name''' – Simulator name.
*** '''Simulator options''' – Simulator options.
**** '''Absolute tolerance''' – Absolute tolerance.
**** '''Relative tolerance''' – Relative tolerance.
**** '''Statistics mode''' – Statistics mode.
**** '''Integration method''' – Integration method (ADAMS or BDF)
**** '''Inner linear solver type''' – Inner linear solver type
**** '''Jacobian approximation type''' – Jacobian approximation type
**** '''Steps limit''' – Limitation for solver steps count
**** '''Minimum time step''' – Minimum time step.
**** '''Maximum time step inverted''' – 1 / maximum time step.
**** '''Mu''' – Upper bandwidth of Banded Jacobian
**** '''Ml''' – Lower bandwidth of Banded Jacobian
**** '''Detect incorrect numbers (NaNs and Infs''' – If true then simulation will end when NaN or Infinity encountered
*** '''Code generation type''' – Type of code generation: if auto then BioUML will try to choose by itself.
*** '''Algebraic solver name''' – Name of algebraic solver which will be used
*** '''Algebraic Solver parameters''' – Parameters of algebraic solver which will be used
**** '''Maximum iterations''' – Maximum iterations
**** '''Function tolerance''' – Function tolerance
**** '''Minimal gradient tolerance''' – Minimal gradient tolerance
**** '''Points tolerance''' – Points tolerance

[[Category:Analyses]]
[[Category:DAE models (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:DAE-models-Parameter-fitting-icon.png]] Parameter fitting
+:[[File:Parameter-fitting-Parameter-fitting-icon.png]] Parameter fitting
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 20: / Line 20: @@
 * '''Result''' – Result
 * '''Simulation engine''' – Simulation engine
-** '''Engine type''' – Engine type.
+** '''Selected engine''' – Selected simulation engine.
-** '''Engine options''' – Engine options.
+** '''Java simulation engine''' – Deterministic simulation engine to solve system of odinary differential equations.
 *** '''Initial time''' – Initial time.
 *** '''Completion time''' – Completion time.
@@ Line 38: / Line 38: @@
 **** '''Mu''' – Upper bandwidth of Banded Jacobian
 **** '''Ml''' – Lower bandwidth of Banded Jacobian
-**** '''Detect incorrect numbers (NaNs and Infs''' – If true then simulation will end when NaN or Infinity encountered
+**** '''Detect incorrect numbers (NaNs and Infs)''' – If true then simulation will end when NaN or Infinity encountered
 *** '''Code generation type''' – Type of code generation: if auto then BioUML will try to choose by itself.
 *** '''Constraints violation''' – How to handle constraints violation in the model.
@@ Line 50: / Line 50: @@
 [[Category:Analyses]]
-[[Category:DAE models (analyses group)]]
+[[Category:Parameter fitting (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]

@@ Line 12: / Line 12: @@
 * '''Input diagram''' – Input diagram
 * '''Experiment table''' – Experiment table
 * '''Algorithm''' – Algorithm
 ** '''type''' – type
 ** '''Iterations number''' – Iterations number
 ** '''Survival size''' – Survival size
 * '''Result''' – Result
 * '''Simulation engine''' – Simulation engine
@@ Line 40: / Line 40: @@
 **** '''Detect incorrect numbers (NaNs and Infs''' – If true then simulation will end when NaN or Infinity encountered
 *** '''Code generation type''' – Type of code generation: if auto then BioUML will try to choose by itself.
 *** '''Algebraic solver name''' – Name of algebraic solver which will be used
 *** '''Algebraic Solver parameters''' – Parameters of algebraic solver which will be used