# sbmlutils

> Python utilities for the Systems Biology Markup Language (SBML)

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

## Documentation

- [Home](https://matthiaskoenig.github.io/sbmlutils/index.md): `sbmlutils` is a collection of python utilities for working with models in the Systems Biology Markup Language (SBML), built on libsbml.
- [Installation](https://matthiaskoenig.github.io/sbmlutils/installation.md): `sbmlutils` requires python >= 3.11 and is available from pypi.
- [References](https://matthiaskoenig.github.io/sbmlutils/references.md): `sbmlutils` implements the specifications of the Systems Biology Markup Language.
- [Contributing](https://matthiaskoenig.github.io/sbmlutils/development.md): Contributions are welcome.

## User guide

- [Model creation](https://matthiaskoenig.github.io/sbmlutils/creation.md): A model is a python object.
- [Units](https://matthiaskoenig.github.io/sbmlutils/units.md): Every quantity in a model has a unit, and SBML requires those units to be declared as `UnitDefinition` elements built from base unit kinds, exponents, scales and multipliers.
- [Annotations](https://matthiaskoenig.github.io/sbmlutils/annotations.md): An element named `glc` means nothing to a machine.
- [Notes](https://matthiaskoenig.github.io/sbmlutils/notes.md): SBML notes are the human readable description of an element.
- [Validation](https://matthiaskoenig.github.io/sbmlutils/validation.md): libsbml validates a document against the SBML specification and reports what it finds as a list of errors.
- [Reading and writing](https://matthiaskoenig.github.io/sbmlutils/io.md): `sbmlutils.io` wraps the libsbml reader and writer, so a model is read from a path, a string or a URL and written with the metadata SBML expects.
- [Model composition](https://matthiaskoenig.github.io/sbmlutils/comp.md): Large models are built from smaller ones.
- [Flux balance constraints](https://matthiaskoenig.github.io/sbmlutils/fbc.md): The SBML fbc package turns a reaction network into a constraint based model: every reaction gets a lower and an upper flux bound, an objective says what to optimize, and gene products link reactions to the genes which encode them.
- [Distributions and uncertainties](https://matthiaskoenig.github.io/sbmlutils/distrib.md): A parameter of a model is rarely a single number.
- [COMBINE archives](https://matthiaskoenig.github.io/sbmlutils/omex.md): A model is rarely the whole story: a study consists of one or more models, the simulation experiments which were run on them, the data and the figures.
- [Reports](https://matthiaskoenig.github.io/sbmlutils/reports.md): An SBML file is XML: complete, but not readable.
- [Converters](https://matthiaskoenig.github.io/sbmlutils/converters.md): An SBML model is a description, not a program.
- [Interpolation](https://matthiaskoenig.github.io/sbmlutils/interpolation.md): A model often has to follow measured data: a plasma concentration over time, a dose response curve, an input which was recorded rather than computed.
- [Visualization](https://matthiaskoenig.github.io/sbmlutils/visualization.md): A reaction network is easier to check as a picture than as XML.

## API reference

- [Overview](https://matthiaskoenig.github.io/sbmlutils/api/index.md): The API reference is generated from the docstrings of the package.
- [factory](https://matthiaskoenig.github.io/sbmlutils/api/factory.md): Factory for creating SBML objects.
- [io](https://matthiaskoenig.github.io/sbmlutils/api/io.md): Helper functions for input/output (IO).
- [validation](https://matthiaskoenig.github.io/sbmlutils/api/validation.md): Helpers for validation and checking of SBML and libsbml operations.
- [parser](https://matthiaskoenig.github.io/sbmlutils/api/parser.md): Parse Models in internal model format.
- [notes](https://matthiaskoenig.github.io/sbmlutils/api/notes.md): Module for notes.
- [reaction_equation](https://matthiaskoenig.github.io/sbmlutils/api/reaction_equation.md): Module for parsing reaction equation strings.
- [biomodels](https://matthiaskoenig.github.io/sbmlutils/api/biomodels.md): Utilities for downloading biomodel models.
- [cytoscape](https://matthiaskoenig.github.io/sbmlutils/api/cytoscape.md): Module for visualization in Cytoscape.
- [console](https://matthiaskoenig.github.io/sbmlutils/api/console.md): Shared rich console.
- [log](https://matthiaskoenig.github.io/sbmlutils/api/log.md): Logging of the package.
- [utils](https://matthiaskoenig.github.io/sbmlutils/api/utils.md): Utility functions.
- [comp](https://matthiaskoenig.github.io/sbmlutils/api/comp.comp.md): Utilities for the creation and work with comp models.
- [flatten](https://matthiaskoenig.github.io/sbmlutils/api/comp.flatten.md): Helpers for model flattening.
- [odefac](https://matthiaskoenig.github.io/sbmlutils/api/converters.odefac.md): Convert SBML models to ODE systems for various programming languages.
- [xpp](https://matthiaskoenig.github.io/sbmlutils/api/converters.xpp.md): XPP ode to SBML file converter.
- [copasi](https://matthiaskoenig.github.io/sbmlutils/api/converters.copasi.md): Helpers to work with COPASI files.
- [mathml](https://matthiaskoenig.github.io/sbmlutils/api/converters.mathml.md): Helper functions for evaluation of mathml expressions.
- [interpolation](https://matthiaskoenig.github.io/sbmlutils/api/data.interpolation.md): Create files for interpolation of datasets.
- [fbc](https://matthiaskoenig.github.io/sbmlutils/api/fbc.fbc.md): Helper functions for working with FBC and cobrapy models.
- [cobra](https://matthiaskoenig.github.io/sbmlutils/api/fbc.cobra.md): cobrapy based helper methods.
- [layout](https://matthiaskoenig.github.io/sbmlutils/api/layout.layout.md): Utilities for the creation and work with layout models.
- [merge](https://matthiaskoenig.github.io/sbmlutils/api/manipulation.merge.md): Merging of SBML models.
- [annotator](https://matthiaskoenig.github.io/sbmlutils/api/metadata.annotator.md): Annotation of SBML models.
- [validator](https://matthiaskoenig.github.io/sbmlutils/api/metadata.validator.md): Validation of the annotations of a model against the registry.
- [miriam](https://matthiaskoenig.github.io/sbmlutils/api/metadata.miriam.md): MIRIAM qualifiers of libsbml.
- [sbmlinfo](https://matthiaskoenig.github.io/sbmlutils/api/report.sbmlinfo.md): Creates dictionary of information for given model.
- [sbmlreport](https://matthiaskoenig.github.io/sbmlutils/api/report.sbmlreport.md): SBML report using https://sbml4humans.de.
- [units](https://matthiaskoenig.github.io/sbmlutils/api/report.units.md): Helper functions for formating and rendering units.
- [mathml](https://matthiaskoenig.github.io/sbmlutils/api/report.mathml.md): Rendering of formulas and Content MathML.

## Optional

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