Metadata-Version: 2.1
Name: cobramod
Version: 0.5.4a2
Summary: Python package for pathway-centric modification and extension of genome-scale metabolic networks
Home-page: https://github.com/Toepfer-Lab/cobramod
Author: Stefano Camborda La Cruz, Jan-Niklas Weder, Nadine Töpfer
Author-email: toepfer@ipk-gatersleben.de
License: GPL v.3.0
Project-URL: Documentation, https://cobramod.readthedocs.io/
Project-URL: Bug Tracker, https://github.com/Toepfer-Lab/cobramod/issues
Keywords: genome-scale metabolic model,constraint-based modelling,COBRApy,Eschermetabolic model curation
Platform: 
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7.4
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: cobra (>=0.18.1)
Requires-Dist: requests (>=2.24.0)
Requires-Dist: Escher (>=1.7.3)
Requires-Dist: openpyxl (>=3.0.7)
Requires-Dist: webcolors (>=1.11.1)

.. image:: https://img.shields.io/github/license/Toepfer-Lab/cobramod
   :alt: GitHub
.. image:: https://img.shields.io/readthedocs/cobramod/latest
   :alt: Read the Docs (version)

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

.. image:: https://raw.githubusercontent.com/Toepfer-Lab/cobramod/master/docs/source/img/logo.png
  :width: 600
  :align: center

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.

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 <https://escher.github.io/>`_ 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 <https://cobramod.readthedocs.io/>`_ for more
information.

License
------------
CobraMod is licensed under the GPL-3 License. Read `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 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.


