cobramod 0.5.4a2

Python package for pathway-centric modification and extension of genome-scale metabolic networks

CobraMod: A pathway-centric curation tool for constraint-based metabolic models

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.

CobraMod will use and parse the exact information from the metabolic pathway information. 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 according to the data

• assignment of genes

• mass balance of reactions

• reaction reversibility

• capability to carry non-zero fluxes

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.

Installation

CobraMod can easily be installed using pip.

pip install cobramod

Functions

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

Check the documentation for more information.

License

CobraMod is licensed under the GPL-3 License. Read LICENSE for more information.

Development

You can contribute to CobraMod by cloning the repository and installing it in developer mode using pip:

pip install -e .

A conda environment file is supplied (environment.yml). This file has all dependencies that we use to ensure the reproducibility of the package. To report bugs and suggestions, please create an issue using the corresponding tags at https://github.com/Toepfer-Lab/cobramod/issues.

We encourage pull requests. CobraMod uses unit testing and new tests are welcome.