Difference between revisions of "Parameter fitting (analysis)"

From BioUML platform
Jump to: navigation, search
m (Protected "Parameter fitting (analysis)": Autogenerated page (‎[edit=sysop] (indefinite)))
(Automatic synchronization with BioUML)
 
(One intermediate revision by one user not shown)
Line 1: Line 1:
 
;Analysis title
 
;Analysis title
:[[File:DAE-models-Parameter-fitting-icon.png]] Parameter fitting
+
:[[File:Parameter-fitting-Parameter-fitting-icon.png]] Parameter fitting
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
Line 12: Line 12:
 
* '''Input diagram''' – Input diagram
 
* '''Input diagram''' – Input diagram
 
* '''Experiment table''' – Experiment table
 
* '''Experiment table''' – Experiment table
 +
* '''Regime''' – Regime
 +
* '''Data column''' – Data column
 
* '''Algorithm''' – Algorithm
 
* '''Algorithm''' – Algorithm
 
** '''type''' – type
 
** '''type''' – type
 
** '''Iterations number''' – Iterations number
 
** '''Iterations number''' – Iterations number
 
** '''Survival size''' – Survival size
 
** '''Survival size''' – Survival size
* '''Parameters group''' – Parameters group
 
** '''Parameters''' – Parameters
 
 
* '''Result''' – Result
 
* '''Result''' – Result
 
* '''Simulation engine''' – Simulation engine
 
* '''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.
 
*** '''Initial time''' – Initial time.
 
*** '''Completion time''' – Completion time.
 
*** '''Completion time''' – Completion time.
Line 38: Line 38:
 
**** '''Mu''' – Upper bandwidth of Banded Jacobian
 
**** '''Mu''' – Upper bandwidth of Banded Jacobian
 
**** '''Ml''' – Lower 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.
 
*** '''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.
 +
*** '''Fast reactions handling''' – Method to handle fast reactions: either as separate ODE system with very fast rate or as algebraic system.
 
*** '''Algebraic solver name''' – Name of algebraic solver which will be used
 
*** '''Algebraic solver name''' – Name of algebraic solver which will be used
 
*** '''Algebraic Solver parameters''' – Parameters of algebraic solver which will be used
 
*** '''Algebraic Solver parameters''' – Parameters of algebraic solver which will be used
Line 48: Line 50:
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:DAE models (analyses group)]]
+
[[Category:Parameter fitting (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Parameter-fitting-Parameter-fitting-icon.png Parameter fitting
Provider
Institute of Systems Biology
Class
ParameterFitting
Plugin
biouml.plugins.optimization (Optimization plug-in)

[edit] Parameters:

  • Input diagram – Input diagram
  • Experiment table – Experiment table
  • Regime – Regime
  • Data column – Data column
  • Algorithm – Algorithm
    • type – type
    • Iterations number – Iterations number
    • Survival size – Survival size
  • Result – Result
  • Simulation engine – Simulation engine
    • Selected engine – Selected simulation engine.
    • Java simulation engine – Deterministic simulation engine to solve system of odinary differential equations.
      • 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.
      • Constraints violation – How to handle constraints violation in the model.
      • Fast reactions handling – Method to handle fast reactions: either as separate ODE system with very fast rate or as algebraic system.
      • 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
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox