API reference¶
The API reference is generated from the docstrings of the package.
sbmlsim¶
The top level modules: data, formulas, units and the shared output.
| module | description |
|---|---|
| data | Data objects referencing simulation results and datasets, the input of plots and calculations |
| mathml | evaluation of the formulas of Data functions |
| 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.calculation | calculations on simulation results |
| simulation.base | base classes shared by the simulation objects |
| 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 FitMappingCollection, 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.display | the sections of the console output of a fit: the problem, the parameters, the settings and the data |
| 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.identifiability | profile_likelihood, the confidence intervals and the classification of the parameters from the profiles |
| fit.fisher | fisher_information, the standard errors, correlations and constrained directions from one jacobian |
| fit.helpers | helpers for fitting |
| fit.petab_omex | COMBINE archives of PEtab problems |
PEtab v2, see PEtab.
| module | description |
|---|---|
| fit.petab_v2.export | writing an OptimizationProblem as a PEtab v2 problem |
| fit.petab_v2.reader | reading a PEtab v2 problem back into a fit problem |
| fit.petab_v2.extension | the sbmlsim block of the problem, i.e., what PEtab does not express |
| fit.petab_v2.observables | the model a fit simulates when an observable is a formula |
| fit.petab_v2.symbols | the identifiers and symbols shared by the PEtab layer |
| fit.petab_v2.gaps | the catalogue of the differences between a fit and its PEtab problem |
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.testsuite¶
The semantic cases of the SBML Test Suite, see SBML Test Suite.
| module | description |
|---|---|
| testsuite.cases | SemanticCase and SemanticSuite, the cases of a release on disk and its download |
| testsuite.runner | run_case, simulating a case, and CaseStatus, the outcomes a case can have |
| testsuite.comparison | comparing the results of a case within its tolerances |
| testsuite.report | TestSuiteReport, the interactive report of a run |
sbmlsim.comparison¶
| module | description |
|---|---|
| comparison.diff | numerical comparison of simulation results from different simulators |