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:
Retrieve metabolic pathway information from a database
cobramod.get_data()
Transform stored data into COBRApy objects
cobramod.create_object()
Add metabolites from multiple sources
cobramod.add_metabolites()
Add reactions from multiple sources
cobramod.add_reactions()
Test reaction capability to carry a non-zero flux
cobramod.test_non_zero_flux()
Add pathway to a model
cobramod.add_pathway()
Automatic cross-referencing
cobramod.add_crossreferences()
Testing for Memote compliance
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
.