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 |
| distrib | the grammar of the distrib formulas of the fitted parameters (normal, lognormal, uniform, truncated), without a simulator |
| licenses | the license texts of a model (CC BY-SA 4.0, MIT) and write_license, which writes them byte for byte |
| engine | Engine, the engines which simulate a model, roadrunner, COPASI and AMICI, the imports of the optional COPASI and AMICI and the directory of the compiled models of AMICI the workers of a pool load from |
| sbml_math | the math of SBML as sympy expressions and numpy functions, the math of the events of a model |
| serialization | JSON serialization of experiments |
| utils | timing and other helpers |
| parallel | the process pools of sbmlsim: the start method, the kept pools and the caches of the workers |
| project | Project, a model package: its model variants and factory, experiments, fits and their records, scans and uncertainty analyses, which the run layer resolves, with the settings of its simulator, figures, checks and release |
| project_checks | the checks of a model package as functions over a Project |
| events | the events of a run as JSON lines |
| atomic | atomic writes of files and directories |
| cgroup | the CPU quota of the cgroup of the process |
| console | shared rich console |
| display | the output of scripts: sections, key/value blocks and links which the terminal opens with a click |
| log | logging of the package |
sbmlsim.model¶
Models and the changes of a model, see Models.
| module | description |
|---|---|
| model.model | AbstractModel, the model of a simulation experiment with its changes and selections |
| model.model_sbml | SBMLModel, the SBML model independent of its engine, and load_model, which loads a model in an engine |
| model.model_roadrunner | RoadrunnerSBMLModel, the roadrunner instance of an SBML model with its units and parameter changes |
| model.model_copasi | CopasiSBMLModel, an SBML model loaded in COPASI, with the values and selections of roadrunner |
| model.model_amici | AmiciSBMLModel, an SBML model compiled with AMICI, with the values and selections of roadrunner, the cache of the compiled models and the refused features |
| model.comparisons | the comparisons of the maths of a model, which COPASI and AMICI shift at their threshold |
| model.model_resources | Source, resolving the source of a model, i.e., a file or the SBML itself |
| model.event_rows | with_event_markers, the markers which tell the rows of the events of the model, and at_event_times, which gives the two rows of an event in the steps of the integrator the time of the event |
| model.symbols | ModelSymbols, the entities of a model a simulation changes and its initial assignments |
| model.provenance | the record of what was added to a derived model, i.e. the compiled networks, and its inverse |
sbmlsim.simulation¶
Definition of simulations, see Simulations and Parameter scans and Observables.
| module | description |
|---|---|
| simulation.definition | Simulation, Change and SteadyState, a simulation with its changes, with units |
| simulation.scan | Scan and Dimension, a simulation over dimensions of values, simulations and models |
| simulation.observables | Formula, PK and Custom, what a scan computes from every simulation |
| simulation.sampling | the sampler: distributions, references and the designs of a scan, of the sensitivity analyses, of a fit and of a population |
sbmlsim.simulator, sbmlsim.task¶
Execution of simulations.
| module | description |
|---|---|
| simulator.simulator | Simulator, simulations and scans of models, serially or in a pool of processes |
| simulator.plan | Plan, a simulation compiled against a model, without units |
| simulator.executor | execute, running a plan on roadrunner with the semantics of PEtab v2 |
| simulator.executor_copasi | execute, running a plan on COPASI with the semantics of the roadrunner executor, and the known differences |
| simulator.executor_amici | execute, running a plan on AMICI with the semantics of the roadrunner executor, the executor firing the events, and the known differences |
| simulator.segments | simulate_segments, the segments of a plan between its changes, shared by the executors of COPASI and AMICI |
| simulator.engines | execute_plan, running a plan with the executor of the engine of a model |
| simulator.changes | the changes of a plan and the events a change fires, shared by the engines |
| simulator.formula | the formulas of the changes of a simulation |
| simulator.worker | the chunks of a scan, run on one plan and one model in a worker |
| simulator.shared | the large arrays of a chunk result in shared memory, from a worker to the parent |
| simulator.observables | the compiled observables of a scan and their evaluation on the native solutions |
| simulator.pk | the non-compartmental analysis of a PK observable with pkpdutils |
| 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 |
| experiment.progress | RunProgress and PhaseClock, the progress of a run of experiments and the seconds of their phases |
| experiment.draws | UncertaintySettings, UncertaintyRun and apply_uncertainty, the experiments over draws of the fitted parameters with bands; check_fit_parameters of the variants of a project |
| experiment.sids | to_sid, the SId of a text such as a label of the data, a key of an experiment |
| result.timecourse | TimecourseResult, the array of the selections of a single timecourse simulation |
| result.scan | ScanResult, the result of a scan as an xarray dataset with units, and the functions of a point: its timecourse with the state after a change, the start and end values, the band of the draws |
| result.netcdf | the compressed netCDF files of ScanResult and SensitivityResult |
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.points | the lines, colours, legend labels and colour bars of a curve over the points of a scan, and the quantiles of a band |
| 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.parameter_mapping | which parameter writes which entity in which simulation, the coverage of versioned parameters |
| fit.derived | derived changes of a simulation, the protocol a network before the simulation implements, and the summary of a hook for the console and the report |
| 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.variability | Variability, the relative distributions of the subjects of a fit problem; subject_predictions and predictive_check, the visual predictive check of the mappings with virtual groups |
| fit.helpers | helpers for fitting |
| fit.petab_omex | COMBINE archives of PEtab v2 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.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 |
| fit.petab_v2.conversion | the conversion of a problem of PEtab v1 and its simulations to PEtab v2 |
| fit.petab_v2.likelihood | the log-likelihood and its gradient, chi2 and the priors, the noise models of PEtab v2 |
| fit.petab_v2.testsuite | the PEtab Test Suite: its cases of models and of math, and their comparison |
| fit.petab_v2.benchmark | the PEtab benchmark collection: its problems converted to PEtab v2, simulated and compared with the collection and with AMICI |
| fit.petab_v2.sciml | the networks of a PEtab SciML problem read into Hybridization objects |
| fit.petab_v2.sciml_export | the hybridizations of a problem written as PEtab SciML |
sbmlsim.sensitivity¶
Local and global sensitivity analysis, see Sensitivity analysis.
| module | description |
|---|---|
| sensitivity.indices | the local, Sobol, FAST and Morris indices of the result of a scan |
| sensitivity.result | the SensitivityResult with the indices, classify and netCDF |
| sensitivity.classification | classification of sensitivities and uncertainties |
| sensitivity.plots | heatmap, bars of the indices and the plane of Morris |
| sensitivity.uncertainty | bands and distributions of a scan over draws |
| sensitivity.parameters | the table of the parameters of an analysis, as sbmlsim 0.8 wrote it |
| sensitivity.runner | the sensitivity analyses of a project over the groups of its simulations, with the files of sbmlsim 0.8.5 |
sbmlsim.release¶
The release of a project as a repository of its own, see Release.
| module | description |
|---|---|
| release.settings | ReleaseSettings and Author, the release metadata of a project, standard library only |
| release.archive | the COMBINE archive of the models of a release: the SBML, its ODEs and antimony, the licenses |
| release.workflow | the build of a release into an output and its publishing, build_release and publish_release |
| release.source | the source repository and the release repository of a model, the checks before a build |
| release.project | the project files of a release repository written from templates |
| release.build | the build of a release repository: the analyses of the release in its own environment |
| release.notes | the release notes of a release repository |
| release.docs | the documentation site and the README of a release repository |
| release.manifest | the manifest release.json of a release and the removal of what the release did not build |
| release.publish | the publishing of a built release: commit, tag, Pages, Docker image and GitHub release |
| release.hooks | ReleaseHook, what a framework adds to the release of a model package |
| release.cli | the command line python -m sbmlsim.release |
sbmlsim.credibility¶
The credibility of a model for its contexts of use, see Credibility.
| module | description |
|---|---|
| credibility.declaration | Credibility, ContextOfUse, Domain, Evidence, QuantityOfInterest and the acceptance rules, the declaration of the contexts of use of a model, and metadata_fields, the fields of the metadata a domain claims |
| credibility.risk | the model risk of the influence and the consequence, the default acceptance and the default minimum of points |
| credibility.factors | FACTORS, the credibility factors of ASME V&V 40 and their status |
| credibility.extensions | EvidenceExtension, the evidence a project adds to the credibility, and the sections of the extensions in the records |
| credibility.selection | select, the data points of the evidence of the contexts of use |
| credibility.records | evaluate_fits and mapping_table, the data points of the adopted fits with the recorded kinds of their mappings |
| credibility.lock | the lock of the evidence, written into an out and compared with the one of the project |
| credibility.check | check_declaration, the static check of a declaration against the adopted fits |
| credibility.uncertainty | propagate_fits, the parameter uncertainty of the adopted fits propagated to the decisive predictions |
| credibility.variability | predictive_checks, the visual predictive check of the decisive points with the variability of the subjects |
| credibility.cross_validation | cross_validate, the leave-one-study-out cross-validation of an adopted fit |
| credibility.verification | verify, the decisive predictions with tightened tolerances and a second integration method, and the open checks, Check and register_check |
| credibility.battery | run_battery, the checks of the variants of a model, and BatteryHook, the simulations and checks a project adds |
| credibility.assessment | assess, the assessment of the contexts of use on the adopted fits, CredibilityAssessment and its record |
| credibility.report | write_outputs, the record, the tables and the report of an assessment |
| credibility.scorecard | scorecard and compare, the assessments of many models and their regressions against a baseline |
sbmlsim.sciml¶
The neural networks of hybrid problems, see PEtab SciML. The package needs the extra sciml.
| module | description |
|---|---|
| sciml | the package: Network, Hybridization, NetworkInput, NetworkPattern, compile_network, network_fit_parameters, nominal_parameters, the id functions and the errors |
| sciml.network | Network, the architecture and the arrays of a network, its forward pass and the ids of its elements, inputs and outputs |
| sciml.hybridization | Hybridization, where a network sits, its inputs and outputs, its fit parameters and the derived changes of a network before the simulation |
| sciml.compiler | compile_network, a network in the right hand side or in an observable written into the model as assignment rules |
| sciml.formula | the math of SBML as sympy expressions, read with libsbml and sbmlmath, and written back, for the compiler and the hybridization |
| sciml.parameters | the nominal values and the fit parameters of a network per network, layer or array |
| sciml.interpreter | the walk over the forward pass of the NN YAML with a backend |
| sciml.backend | the numpy backend of the forward pass and the sympy backend of the compiler |
| sciml.layers | the layers and functions of PEtab SciML with the backends they support |
| sciml.errors | the errors of the package |
| sciml.testsuite | the PEtab SciML Test Suite: its cases, their comparison and the round trip |
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 |
| testsuite.submission | write_submission, the archive with the results of a run for the SBML Test Suite Database |
| testsuite.cache | the download and the cache of a test suite, shared by the SBML Test Suite, the PEtab test suite and the PEtab SciML test suite |
| testsuite.baseline | the baseline of the PEtab test suites and of the benchmark collection, i.e. the cases which do not pass with their reasons |
sbmlsim.comparison¶
| module | description |
|---|---|
| comparison.diff | numerical comparison of simulation results from different simulators |