cobramod 1.0.0

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](https://opencobra.github.io/cobrapy/) and offers a comprehensible set of functions for semi-automated network extension, curation and visualization. CobraMod supports all databases from the [BioCyc collection](https://biocyc.org/), the [KEGG database](https://www.genome.jp/kegg/), and the [BiGG Models repository](http://bigg.ucsd.edu/) and can directly interact with Escher for pathway and flux visualization.

This package converts pathway information into native COBRApy objects and quality-checks them while 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

• 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](https://escher.github.io/).

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](https://cobramod.readthedocs.io/) for more information.

License

CobraMod is licensed under the GPL-3 License. Read the [LICENSE](https://github.com/Toepfer-Lab/cobramod/blob/master/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 contains all the dependencies to ensure reproducibility of the package. We encourage pull requests. CobraMod uses unit testing and new tests are welcome.

To report bugs and suggestions, please create an issue using the corresponding tags at <https://github.com/Toepfer-Lab/cobramod/issues>.