Difference between revisions of "Sample population (analysis)"
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* '''Diagram''' – Diagram. | * '''Diagram''' – Diagram. | ||
* '''Experimental data''' – Experimental data | * '''Experimental data''' – Experimental data | ||
| − | * '''Initial | + | * '''Initial values''' – Mean and variance values for estimated variables. |
* '''Result path''' – Result Path. | * '''Result path''' – Result Path. | ||
* '''Population size per chain''' – Population size per chain. | * '''Population size per chain''' – Population size per chain. | ||
* '''Preliminary steps''' – Preliminary steps | * '''Preliminary steps''' – Preliminary steps | ||
* '''Acceptance rate''' – Acceptance rate | * '''Acceptance rate''' – Acceptance rate | ||
| + | * '''Random seed''' – Seed for random algorithms. 0 means seed defined by time (recommended) | ||
* '''Observed variables''' – Observed variables | * '''Observed variables''' – Observed variables | ||
* '''Variables to estimate''' – Variables to estimate | * '''Variables to estimate''' – Variables to estimate | ||
| + | * '''Simulation options''' – Simulation options | ||
| + | ** '''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 | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Sample population
- Provider
- Institute of Systems Biology
- Class
PopulationSampling- Plugin
- biouml.plugins.pharm (Support for Pharmocological models)
[edit] Description
Sample population.
[edit] Parameters:
- Diagram – Diagram.
- Experimental data – Experimental data
- Initial values – Mean and variance values for estimated variables.
- Result path – Result Path.
- Population size per chain – Population size per chain.
- Preliminary steps – Preliminary steps
- Acceptance rate – Acceptance rate
- Random seed – Seed for random algorithms. 0 means seed defined by time (recommended)
- Observed variables – Observed variables
- Variables to estimate – Variables to estimate
- Simulation options – Simulation options
- 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
