IntroductionΒΆ

CobraMod is a Python 3 open-source package for pathway-centric curation of genome-scale metabolic models (GEMs). It builds upon the COBRApy toolbox and offers a comprehensible set of functions for semi-automated network extension, curation and visualization. CobraMod supports all databases from the BioCyc collection, the KEGG database, and the BiGG Models repository and can directly interact with Escher for pathway and flux visualization.

This package converts pathway information into native COBRApy objects and quality-checks them before adding them to the model. This includes testing for:

  • duplicate elements

  • correct chemical formula

  • mass balance of reactions

  • reaction reversibility

  • capability to carry non-zero fluxes

  • MEMOTE compliance

  • available cross-references

  • adding available gene information

CobraMod offers user-friendly tracking of the curation process with summary output and log files and customized pathway and flux visualization with Escher. CobraMod uses Escher for visualizing pathways and flux distributions and offers several customization options.

Example of the visualization method

This pathway representation uses Escher. We created three fictive reactions and added them to a toy model. The arrows represent the flux of the reactions. Using CobraMod we visualize the pathway and set colors for the fluxes. Red color represents negative fluxes and green positive fluxes.

This package offers multiple functions for modifying and extending GEMs:

Users can add the biochemical data through different methods:

  • Using COBRApy objects

  • Using a text file with database-specific identifiers for the metabolites, reactions, or pathways.

  • Using a single string with the database-specific identifier of the object

  • Using a text file or string with user-defined metabolite, reaction information

CobraMod includes the class cobramod.Pathway which inherits all methods of the COBRApy cobra.core.group.Group and additionally includes the method cobramod.Pathway.visualize() for creating pathway and flux maps.

For more information see the docstrings of the respective functions using help() or read the documentation.

To see all metabolic pathway databases that are currently supported by CobraMod, load and print cobramod.available_databases.