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