Difference between revisions of "Parameter fitting (analysis)"
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;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[File:Parameter-fitting-Parameter-fitting-icon.png]] Parameter fitting |
;Provider | ;Provider | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
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* '''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 | ||
| − | |||
| − | |||
* '''Result''' – Result | * '''Result''' – Result | ||
* '''Simulation engine''' – Simulation engine | * '''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. | *** '''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 | ||
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[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[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
- 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
