Difference between revisions of "Parameter fitting (analysis)"
From BioUML platform
m (Protected "Parameter fitting (analysis)": Autogenerated page ([edit=sysop] (indefinite))) |
(Automatic synchronization with BioUML) |
||
| 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 | ||
| − | |||
| − | |||
* '''Result''' – Result | * '''Result''' – Result | ||
* '''Simulation engine''' – Simulation engine | * '''Simulation engine''' – Simulation engine | ||
| Line 40: | Line 40: | ||
**** '''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 | ||
Revision as of 16:32, 12 March 2019
- Analysis title
Parameter fitting
- Provider
- Institute of Systems Biology
- Class
ParameterFitting- Plugin
- biouml.plugins.optimization (Optimization plug-in)
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
- Engine type – Engine type.
- Engine options – Engine options.
- 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
