Difference between revisions of "Apply events (analysis)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
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* '''Result path''' – Path to the diagram for analysis. | * '''Result path''' – Path to the diagram for analysis. | ||
* '''Simulation parameters''' – Simulation parameters. | * '''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. | *** '''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 | + | **** '''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. | *** '''Constraints violation''' – How to handle constraints violation in the model. | ||
| Line 44: | Line 44: | ||
[[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
Apply events
- Provider
- Institute of Systems Biology
- Class
ApplyEvents- Plugin
- biouml.plugins.modelreduction (Model reduction plug-in)
[edit] Parameters:
- Diagram path – Path to the diagram for analysis.
- Table path – Path to the table for analysis.
- Result path – Path to the diagram for analysis.
- 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
