Difference between revisions of "Steady State (analysis)"

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;Analysis title
 
;Analysis title
:Steady State
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:[[File:Differential-algebraic-equations-Steady-State-icon.png]] Steady State
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|biouml.plugins.modelreduction.SteadyStateAnalysis}}
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;Plugin
 +
:[[Biouml.plugins.modelreduction (plugin)|biouml.plugins.modelreduction (Model reduction plug-in)]]
  
 
==== Description ====
 
==== Description ====
Model steady state finding.
+
Find steady state by simuilating model until steady state.
  
 
==== Parameters: ====
 
==== Parameters: ====
  
* '''Diagram''' – Diagram for analysis.
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* '''Input diagram''' – Input diagram.
* '''Steady state name''' – Steady state name if empty - steady state parameters will be set to default state.
+
* '''Input state''' – Input state
* '''Result diagram''' – Diagram with steady state values.
+
* '''Output type''' – Output type.
* '''Variable names''' (expert) – Variables which values will be used for steady state detection. If no variables selected then all variables will be used
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* '''Result diagram''' – Result diagram.
* '''Relative tolerance''' – Relative tolerance for the steady state checking.
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* '''State''' – Diagram state.
* '''Absolute tolerance''' – Absolute tolerance for the steady state checking.
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* '''Simulation result''' – Simulation result
* '''Validation series size''' (expert) – Size of parameters time series for steady state check.
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* '''Result table''' – Result table
* '''Start search time''' (expert) – Time to start the steady state searching.
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* '''Stady state variables''' – Variables which values will be used for steady state detection. If no variables selected then all variables will be used.
* '''Simulation options''' (expert) – Simulation engine, suitable for chosen diagram.
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* '''Relative tolerance''' – Relative tolerance for steady state.
** '''Engine type''' – Engine type.
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* '''Absolute tolerance''' – Absolute tolerance for steady state.
** '''Engine options''' – Engine options.
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* '''Time points number''' (expert) – Number of consequent time points for steady state detection.
 +
* '''Start time''' (expert) – Start time for steady state detection.
 +
* '''Simulation parameters''' (expert) – Simulation parameters.
 +
** '''Selected engine''' – Selected simulation engine.
 +
** '''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.
 
*** '''Time increment''' – Time increment.
 
*** '''Time increment''' – Time increment.
*** '''Simulator name''' – Simulator name
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*** '''Simulator name''' – Simulator name.
*** '''Simulator options''' – Simulator options
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*** '''Simulator options''' – Simulator options.
 
**** '''Absolute tolerance''' – Absolute tolerance.
 
**** '''Absolute tolerance''' – Absolute tolerance.
 
**** '''Relative tolerance''' – Relative tolerance.
 
**** '''Relative tolerance''' – Relative tolerance.
**** '''Statistics mode''' – Statistics mode
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**** '''Statistics mode''' – Statistics mode.
 
**** '''Integration method''' – Integration method (ADAMS or BDF)
 
**** '''Integration method''' – Integration method (ADAMS or BDF)
 
**** '''Inner linear solver type''' – Inner linear solver type
 
**** '''Inner linear solver type''' – Inner linear solver type
 
**** '''Jacobian approximation type''' – Jacobian approximation type
 
**** '''Jacobian approximation type''' – Jacobian approximation type
 
**** '''Steps limit''' – Limitation for solver steps count
 
**** '''Steps limit''' – Limitation for solver steps count
**** '''Minimum time step''' – minimum time step
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**** '''Minimum time step''' – Minimum time step.
**** '''Maximum time step inversed''' – 1 / maximum time step
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**** '''Maximum time step inverted''' – 1 / maximum time step.
 
**** '''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
 +
*** '''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
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:DAE models (analyses group)]]
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[[Category:Differential algebraic equations (analyses group)]]
 +
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:14, 9 December 2020

Analysis title
Differential-algebraic-equations-Steady-State-icon.png Steady State
Provider
Institute of Systems Biology
Class
SteadyStateAnalysis
Plugin
biouml.plugins.modelreduction (Model reduction plug-in)

[edit] Description

Find steady state by simuilating model until steady state.

[edit] Parameters:

  • Input diagram – Input diagram.
  • Input state – Input state
  • Output type – Output type.
  • Result diagram – Result diagram.
  • State – Diagram state.
  • Simulation result – Simulation result
  • Result table – Result table
  • Stady state variables – Variables which values will be used for steady state detection. If no variables selected then all variables will be used.
  • Relative tolerance – Relative tolerance for steady state.
  • Absolute tolerance – Absolute tolerance for steady state.
  • Time points number (expert) – Number of consequent time points for steady state detection.
  • Start time (expert) – Start time for steady state detection.
  • Simulation parameters (expert) – Simulation parameters.
    • 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
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