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Overview

sbmlutils are python utilities for working with SBML. This python package provides handy features like HTML reports of SBML models, helper functions for model creation and manipulation, interpolation functions to add experimental data to models, or implementation of dynamic flux balance analysis (DFBA) to name a few.

Main features of sbmlutils are

  • SBML report : HTML report of SBML models. This provides overview of the model contents.
  • SBML creator : The modelcreator provides utilities for the creation of SBML models. Supports comp and fbc models. Model information is managed in python data structures which are used to create the models.
  • SBML annotator : Helper functions for the annotation of SBML models. Annotations are hereby defined in separate annotation files with annotations being matched to ids based on regular expression matching.
  • SBML manipulation : Helper functions for the manipulation of existing SBML models, e.g., merging of SBML models.
  • SBML converters : Converters from and to SBML, e.g. xpp.

- SBML interpolation : Helper functions for working with data interpolation in SBML models. .. - DFBA : Simulator for dynamic flux balance analysis (DFBA) of SBML model. For more information see also https://github.com/matthiaskoenig/dfba.

Source code is available from https://github.com/matthiaskoenig/sbmlutils.

To report bugs, request features or asking questions please file an issue.

Installation

The libsbgn-python package is available from pypi and can be installed via:

pip install sbmlutils

For more detailed installation instructions see https://github.com/matthiaskoenig/sbmlutils.

Citation

To cite sbmlutils reference the latest zenodo release available from https://doi.org/10.5281/zenodo.597149.