API reference¶
The API reference is generated from the docstrings of the package.
sbmlsim¶
The top level modules: data, units and the shared output.
| module | description |
|---|---|
| data | Data objects referencing simulation results and datasets, the input of plots and calculations |
| units | unit registry of a model and unit conversions with pint |
| serialization | JSON serialization of experiments |
| utils | timing and other helpers |
| console | shared rich console |
| log | logging of the package |
sbmlsim.model¶
Models and model changes, see Models.
| module | description |
|---|---|
| model.model | AbstractModel, the model of a simulation experiment with its changes and selections |
| model.model_roadrunner | RoadrunnerSBMLModel, the roadrunner instance of an SBML model with its units and parameter changes |
| model.model_change | ModelChange, clamping species and other structural changes |
| model.model_resources | resolving model sources, i.e., files, URNs and URLs |
sbmlsim.simulation¶
Definition of simulations, see Timecourse simulations and Parameter scans.
| module | description |
|---|---|
| simulation.timecourse | Timecourse and TimecourseSim, concatenated timecourses with changes |
| simulation.scan | ScanSim, a simulation over the dimensions of parameter changes |
| simulation.sensitivity | ModelSensitivity, sensitivity scans of parameters and initial conditions |
| simulation.range | ranges of values for scans |
| simulation.change | changes applied to a model before a simulation |
| simulation.algorithm | Algorithm and AlgorithmParameter, the KISAO description of an integrator |
| simulation.kisaos | the KISAO terms of the supported algorithms and parameters |
| simulation.calculation | calculations on simulation results |
| simulation.base | base classes shared by the simulation objects and SED-ML |
| simulation.simulation | AbstractSim, the base of all simulations |
sbmlsim.simulator, sbmlsim.task¶
Execution of simulations.
| module | description |
|---|---|
| simulator.simulation_serial | SimulatorSerial, running timecourses and scans on a roadrunner model |
| task.task | Task, a simulation applied to a model |
sbmlsim.experiment, sbmlsim.result¶
Simulation experiments and their results, see Simulation experiments.
| module | description |
|---|---|
| experiment.experiment | SimulationExperiment, models, datasets, simulations, tasks, data and figures of an experiment |
| experiment.runner | ExperimentRunner, executing experiments and writing their results |
| result.xresult | XResult, simulation results as an xarray dataset with units |
| result.datagenerator | data generators processing results |
| result.report | reports of results |
sbmlsim.plot, sbmlsim.report¶
Figures and reports, see Plots and reports.
| module | description |
|---|---|
| plot.plotting | Figure, Plot, Axis, Curve and their styles, the plot description independent of the backend |
| plot.serialization_matplotlib | rendering of the figures with matplotlib |
| report.experiment_report | HTML and markdown reports of simulation experiments |
sbmlsim.fit¶
Parameter fitting, see Parameter fitting.
| module | description |
|---|---|
| fit.objects | FitParameter, FitMapping, FitData and FitExperiment, the objects of a fit problem |
| fit.optimization | OptimizationProblem, the residuals and cost of a fit problem |
| fit.options | FitSettings and the options of the optimization, i.e., algorithms, residuals, weighting and loss functions |
| fit.parameters | ParameterSet and ParameterSets, the fitted parameters a report is created from |
| fit.result | OptimizationResult, the result of an optimization |
| fit.runner | running optimizations serially or in parallel |
| fit.report | FitReport, the figures and reports of one or more parameter sets |
| fit.cli | FitDefinition and the general command line tools which run and report a fit |
| fit.sampling | sampling of initial parameter values |
| fit.metrics | FitMetrics and the metrics of a fit: PRED, IPRED, residuals, MSE, RMSE, R² and AIC |
| fit.helpers | helpers for fitting |
| fit.petab_omex | COMBINE archives of PEtab problems |
sbmlsim.sensitivity¶
Local and global sensitivity analysis, see Sensitivity analysis.
| module | description |
|---|---|
| sensitivity.analysis | the common analysis of a model, i.e., outputs, observables and the simulation of parameter samples |
| sensitivity.parameters | selection, bounds and distributions of the analysed parameters |
| sensitivity.sensitivity_local | local sensitivities by finite differences |
| sensitivity.sensitivity_sampling | sampling based sensitivity and uncertainty analysis |
| sensitivity.sensitivity_morris | Morris elementary effects screening |
| sensitivity.sensitivity_sobol | variance based Sobol indices |
| sensitivity.sensitivity_fast | Fourier amplitude sensitivity test (FAST) |
| sensitivity.classification | classification of sensitivities and uncertainties |
| sensitivity.plots | plots of the sensitivity results |
sbmlsim.combine¶
SED-ML, NuML and COMBINE archives, see SED-ML and COMBINE archives.
| module | description |
|---|---|
| combine.sedml.parser | SEDMLParser, a SED-ML document into a simulation experiment |
| combine.sedml.runner | executing SED-ML files and COMBINE archives |
| combine.sedml.task | tasks and repeated tasks of SED-ML |
| combine.sedml.data | data descriptions, i.e., NuML, CSV and TSV data |
| combine.sedml.numl | parser for NuML data |
| combine.sedml.report | SED-ML reports |
| combine.sedml.io | reading and writing SED-ML documents |
| combine.datagenerator | data generators of SED-ML |
| combine.mathml | evaluation of MathML expressions |
sbmlsim.interpolation, sbmlsim.comparison¶
| module | description |
|---|---|
| interpolation.interpolation | interpolation of datasets as SBML models |
| comparison.diff | numerical comparison of simulation results from different simulators |