Difference between revisions of "Key Node Sensitivity Analysis"

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(Automatic synchronization with BioUML)
 
(Automatic synchronization with BioUML)
 
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;Analysis title
 
;Analysis title
:[[File:DAE-models-Key-Node-Sensitivity-Analysis-icon.png]] Key Node Sensitivity Analysis
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:[[File:Differential-algebraic-equations-Key-Node-Sensitivity-Analysis-icon.png]] Key Node Sensitivity Analysis
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
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* '''Input diagram''' – Input diagram.
 
* '''Input diagram''' – Input diagram.
 
* '''Experimental data''' – Experimental data
 
* '''Experimental data''' – Experimental data
 +
* '''Key Nodes''' – Key Nodes
 
* '''Type''' – Type
 
* '''Type''' – Type
 
* '''Name column''' – Name column
 
* '''Name column''' – Name column
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* '''Absolute tolerance''' – Absolute tolerance for steady state.
 
* '''Absolute tolerance''' – Absolute tolerance for steady state.
 
* '''Relative tolerance''' – Relative tolerance for steady state.
 
* '''Relative tolerance''' – Relative tolerance for steady state.
 +
* '''Steady state variables''' – Steady state variables
 
* '''Result table''' – Result table
 
* '''Result table''' – Result table
 
* '''Simulation parameters''' – Simulation parameters.
 
* '''Simulation parameters''' – Simulation parameters.
** '''Engine type''' – Engine type.
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** '''Selected engine''' – Selected simulation engine.
** '''Engine options''' – Engine options.
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** '''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.
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**** '''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
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**** '''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
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[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:DAE models (analyses group)]]
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[[Category:Differential algebraic equations (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:14, 9 December 2020

Analysis title
Differential-algebraic-equations-Key-Node-Sensitivity-Analysis-icon.png Key Node Sensitivity Analysis
Provider
Institute of Systems Biology
Class
KeyNodesSensitivityAnalysis
Plugin
biouml.plugins.modelreduction (Model reduction plug-in)

[edit] Parameters:

  • Input diagram – Input diagram.
  • Experimental data – Experimental data
  • Key Nodes – Key Nodes
  • Type – Type
  • Name column – Name column
  • Time column – Time column
  • Data columns – Data columns
  • Absolute tolerance – Absolute tolerance for steady state.
  • Relative tolerance – Relative tolerance for steady state.
  • Steady state variables – Steady state variables
  • Result table – Result table
  • Simulation parameters – 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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