Difference between revisions of "Steady State (analysis)"
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;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[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}} | ||
;Plugin | ;Plugin | ||
:[[Biouml.plugins.modelreduction (plugin)|biouml.plugins.modelreduction (Model reduction plug-in)]] | :[[Biouml.plugins.modelreduction (plugin)|biouml.plugins.modelreduction (Model reduction plug-in)]] | ||
==== Description ==== | ==== Description ==== | ||
| − | + | Find steady state by simuilating model until steady state. | |
==== Parameters: ==== | ==== Parameters: ==== | ||
| − | * ''' | + | * '''Input diagram''' – Input diagram. |
| − | * ''' | + | * '''Input state''' – Input state |
| − | * '''Result diagram''' – Diagram | + | * '''Output type''' – Output type. |
| − | * ''' | + | * '''Result diagram''' – Result diagram. |
| − | * '''Relative tolerance''' – Relative tolerance for | + | * '''State''' – Diagram state. |
| − | * '''Absolute tolerance''' – Absolute tolerance for | + | * '''Simulation result''' – Simulation result |
| − | * ''' | + | * '''Result table''' – Result table |
| − | * '''Start | + | * '''Stady state variables''' – Variables which values will be used for steady state detection. If no variables selected then all variables will be used. |
| − | * '''Simulation | + | * '''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. | *** '''Initial time''' – Initial time. | ||
*** '''Completion time''' – Completion time. | *** '''Completion time''' – Completion time. | ||
*** '''Time increment''' – Time increment. | *** '''Time increment''' – Time increment. | ||
| − | *** '''Simulator name''' – Simulator name | + | *** '''Simulator name''' – Simulator name. |
| − | *** '''Simulator options''' – Simulator options | + | *** '''Simulator options''' – Simulator options. |
**** '''Absolute tolerance''' – Absolute tolerance. | **** '''Absolute tolerance''' – Absolute tolerance. | ||
**** '''Relative tolerance''' – Relative tolerance. | **** '''Relative tolerance''' – Relative tolerance. | ||
| − | **** '''Statistics mode''' – Statistics mode | + | **** '''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''' – Minimum time step. |
| − | **** '''Maximum time step | + | **** '''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: | + | [[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
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
