# sbmlsim

> SBML simulation made easy: simulation experiments, parameter scans, parameter fitting, sensitivity analysis and SED-ML for SBML models

The links below point to the markdown source of the documentation. [llms-full.txt](https://matthiaskoenig.github.io/sbmlsim/llms-full.txt) contains all of it in a single file.

## Documentation

- [Home](https://matthiaskoenig.github.io/sbmlsim/index.md): `sbmlsim` is a collection of python utilities for the simulation of models in the Systems Biology Markup Language (SBML), built on libroadrunner.
- [Installation](https://matthiaskoenig.github.io/sbmlsim/installation.md): `sbmlsim` requires python >= 3.13 and is available from pypi.
- [References](https://matthiaskoenig.github.io/sbmlsim/references.md): `sbmlsim` builds on the standards of the COMBINE community and on the simulation and analysis libraries of the scientific python ecosystem.
- [Contributing](https://matthiaskoenig.github.io/sbmlsim/development.md): Contributions are welcome.

## User guide

- [Models](https://matthiaskoenig.github.io/sbmlsim/models.md): `sbmlsim` simulates models in the Systems Biology Markup Language (SBML) with libroadrunner.
- [Timecourse simulations](https://matthiaskoenig.github.io/sbmlsim/simulation.md): A timecourse simulation integrates the model over a period of time.
- [Parameter scans](https://matthiaskoenig.github.io/sbmlsim/scans.md): A parameter scan runs a simulation for every combination of parameter values.
- [Units](https://matthiaskoenig.github.io/sbmlsim/units.md): Every SBML model declares units for its parameters, species and compartments.
- [Simulation experiments](https://matthiaskoenig.github.io/sbmlsim/experiments.md): A `SimulationExperiment` is the reproducible description of an experiment: the models, the datasets, the simulations, the tasks which apply a simulation to a model, the data derived from the results, and the figures and reports.
- [Data](https://matthiaskoenig.github.io/sbmlsim/data.md): Simulation experiments compare simulations with experimental data.
- [Plots and reports](https://matthiaskoenig.github.io/sbmlsim/plotting.md): Figures of a simulation experiment are described independent of the plotting backend: a `Figure` holds `Plot` panels, a plot has axes and `Curve` objects, and a curve references `Data` with a `Style`.
- [Parameter fitting](https://matthiaskoenig.github.io/sbmlsim/fitting.md): Parameter fitting adjusts model parameters so that the simulations of experiments match the experimental data.
- [Sensitivity analysis](https://matthiaskoenig.github.io/sbmlsim/sensitivity.md): Sensitivity analysis quantifies how the outputs of a model depend on its parameters.
- [SED-ML and COMBINE archives](https://matthiaskoenig.github.io/sbmlsim/sedml.md): The Simulation Experiment Description Markup Language (SED-ML) describes simulation experiments in a tool independent way: the models with their changes, the simulations and tasks, the data generators computed from the results and the plots and reports.

## API reference

- [Overview](https://matthiaskoenig.github.io/sbmlsim/api/index.md): The API reference is generated from the docstrings of the package.
- [data](https://matthiaskoenig.github.io/sbmlsim/api/data.md): Module handling data (experiment and simulation).
- [units](https://matthiaskoenig.github.io/sbmlsim/api/units.md): Manage units and units conversions.
- [serialization](https://matthiaskoenig.github.io/sbmlsim/api/serialization.md): Helpers for JSON serialization of experiments.
- [utils](https://matthiaskoenig.github.io/sbmlsim/api/utils.md): Utility functions.
- [console](https://matthiaskoenig.github.io/sbmlsim/api/console.md): Shared rich console.
- [log](https://matthiaskoenig.github.io/sbmlsim/api/log.md): Logging of the package.
- [model](https://matthiaskoenig.github.io/sbmlsim/api/model.model.md): Models.
- [model_roadrunner](https://matthiaskoenig.github.io/sbmlsim/api/model.model_roadrunner.md): RoadRunner model.
- [model_change](https://matthiaskoenig.github.io/sbmlsim/api/model.model_change.md): Model changes.
- [model_resources](https://matthiaskoenig.github.io/sbmlsim/api/model.model_resources.md): Model resources.
- [timecourse](https://matthiaskoenig.github.io/sbmlsim/api/simulation.timecourse.md): Definition of timecourses and timecourse simulations.
- [scan](https://matthiaskoenig.github.io/sbmlsim/api/simulation.scan.md): Scan simulation.
- [sensitivity](https://matthiaskoenig.github.io/sbmlsim/api/simulation.sensitivity.md): Helpers for calculating model sensitivities and uncertainties.
- [range](https://matthiaskoenig.github.io/sbmlsim/api/simulation.range.md): Module handling ranges.
- [change](https://matthiaskoenig.github.io/sbmlsim/api/simulation.change.md): Module handling changes.
- [algorithm](https://matthiaskoenig.github.io/sbmlsim/api/simulation.algorithm.md): Handling of algorithms and algorithm parameters.
- [kisaos](https://matthiaskoenig.github.io/sbmlsim/api/simulation.kisaos.md): Working with the KISAO ontology.
- [calculation](https://matthiaskoenig.github.io/sbmlsim/api/simulation.calculation.md): Module for performing all the Calculations.
- [base](https://matthiaskoenig.github.io/sbmlsim/api/simulation.base.md): BaseObjects for SED-ML and simulation.
- [simulation](https://matthiaskoenig.github.io/sbmlsim/api/simulation.simulation.md): Abstract base simulation.
- [simulation_serial](https://matthiaskoenig.github.io/sbmlsim/api/simulator.simulation_serial.md): Serial simulator.
- [task](https://matthiaskoenig.github.io/sbmlsim/api/task.task.md): Tasks.
- [experiment](https://matthiaskoenig.github.io/sbmlsim/api/experiment.experiment.md): SimulationExperiments and helpers.
- [runner](https://matthiaskoenig.github.io/sbmlsim/api/experiment.runner.md): Runner for SimulationExperiments.
- [xresult](https://matthiaskoenig.github.io/sbmlsim/api/result.xresult.md): Module for encoding simulation results and processed data.
- [datagenerator](https://matthiaskoenig.github.io/sbmlsim/api/result.datagenerator.md): DataGenerator.
- [report](https://matthiaskoenig.github.io/sbmlsim/api/result.report.md): Reports.
- [plotting](https://matthiaskoenig.github.io/sbmlsim/api/plot.plotting.md): Classes for storing plotting information.
- [serialization_matplotlib](https://matthiaskoenig.github.io/sbmlsim/api/plot.serialization_matplotlib.md): Serialization of Figure object to matplotlib.
- [experiment_report](https://matthiaskoenig.github.io/sbmlsim/api/report.experiment_report.md): Create report of simulation experiments.
- [objects](https://matthiaskoenig.github.io/sbmlsim/api/fit.objects.md): Definition of Objects used in FitProblems and optimization.
- [optimization](https://matthiaskoenig.github.io/sbmlsim/api/fit.optimization.md): Optimization of parameter fitting problem.
- [options](https://matthiaskoenig.github.io/sbmlsim/api/fit.options.md): Main options for the parameter fitting.
- [result](https://matthiaskoenig.github.io/sbmlsim/api/fit.result.md): Result of optimization.
- [runner](https://matthiaskoenig.github.io/sbmlsim/api/fit.runner.md): Module for running parameter optimizations.
- [analysis](https://matthiaskoenig.github.io/sbmlsim/api/fit.analysis.md): Analysis of fitting results.
- [sampling](https://matthiaskoenig.github.io/sbmlsim/api/fit.sampling.md): Sampling of parameter values.
- [rmse](https://matthiaskoenig.github.io/sbmlsim/api/fit.rmse.md): Calculation of statistics.
- [helpers](https://matthiaskoenig.github.io/sbmlsim/api/fit.helpers.md): Helper functions for fitting.
- [petab_omex](https://matthiaskoenig.github.io/sbmlsim/api/fit.petab_omex.md): COMBINE archive for PEtab problems.
- [analysis](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.analysis.md): Sensitivity analysis.
- [parameters](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.parameters.md): Tools and helpers to handle parameters for sensitivity analysis.
- [sensitivity_local](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.sensitivity_local.md): Local sensitivity analysis using finite differences.
- [sensitivity_sampling](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.sensitivity_sampling.md): Sampling-based sensitivity and uncertainty analysis.
- [sensitivity_morris](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.sensitivity_morris.md): Morris sensitivity analysis.
- [sensitivity_sobol](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.sensitivity_sobol.md): Global sensitivity analysis using Sobol indices.
- [sensitivity_fast](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.sensitivity_fast.md): Global sensitivity analysis using FAST (Fourier Amplitude Sensitivity Test).
- [classification](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.classification.md): Classification of sensitivities and uncertainties.
- [plots](https://matthiaskoenig.github.io/sbmlsim/api/sensitivity.plots.md): Plotting functionality for sensitivity analysis.
- [sedml.parser](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.parser.md): SED-ML support for sbmlsim.
- [sedml.runner](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.runner.md): Module with helpers to execute SED-ML files and COMBINE archives.
- [sedml.task](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.task.md): Task trees of SED-ML documents.
- [sedml.data](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.data.md): Reading NUML, CSV and TSV data from DataDescriptions.
- [sedml.numl](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.numl.md): Parser for NuML data.
- [sedml.report](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.report.md): Reports.
- [sedml.io](https://matthiaskoenig.github.io/sbmlsim/api/combine.sedml.io.md): Template functions to run the example cases.
- [datagenerator](https://matthiaskoenig.github.io/sbmlsim/api/combine.datagenerator.md): DataGenerator.
- [mathml](https://matthiaskoenig.github.io/sbmlsim/api/combine.mathml.md): Helper functions for evaluation of MathML expressions.
- [interpolation](https://matthiaskoenig.github.io/sbmlsim/api/interpolation.interpolation.md): Create files for interpolation of datasets.
- [diff](https://matthiaskoenig.github.io/sbmlsim/api/comparison.diff.md): Helpers for numerical comparison of data.

## Optional

- [Repository](https://github.com/matthiaskoenig/sbmlsim): source code, issues and releases.
- [Sitemap](https://matthiaskoenig.github.io/sbmlsim/sitemap.xml): all pages of the rendered site.
- [objects.inv](https://matthiaskoenig.github.io/sbmlsim/objects.inv): the API objects of the reference as a sphinx inventory.