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https://github.com/biosustain/multitfa
Multivariate thermodynamics-based metabolic flux analysis in Python.
https://github.com/biosustain/multitfa
cobrapy fba metabolism multitfa multivariate python3 tfa thermodynamics tmfa
Last synced: about 1 month ago
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Multivariate thermodynamics-based metabolic flux analysis in Python.
- Host: GitHub
- URL: https://github.com/biosustain/multitfa
- Owner: biosustain
- License: apache-2.0
- Created: 2018-12-05T09:39:17.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2023-12-19T01:52:08.000Z (about 1 year ago)
- Last Synced: 2024-11-10T02:28:01.450Z (about 1 month ago)
- Topics: cobrapy, fba, metabolism, multitfa, multivariate, python3, tfa, thermodynamics, tmfa
- Language: Python
- Homepage:
- Size: 70.9 MB
- Stars: 8
- Watchers: 10
- Forks: 2
- Open Issues: 5
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.rst
- Contributing: .github/CONTRIBUTING.rst
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.rst
Awesome Lists containing this project
README
========
multiTFA
========
.. image:: https://img.shields.io/pypi/v/multitfa.svg
:target: https://pypi.org/project/multitfa/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/multitfa.svg
:target: https://pypi.org/project/multitfa/
:alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/multitfa.svg
:target: https://www.apache.org/licenses/LICENSE-2.0
:alt: Apache Software License Version 2.0
.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
:target: .github/CODE_OF_CONDUCT.md
:alt: Code of Conduct
.. image:: https://github.com/biosustain/multitfa/workflows/CI-CD/badge.svg
:target: https://github.com/biosustain/multitfa/workflows/CI-CD
:alt: GitHub Actions
.. image:: https://codecov.io/gh/biosustain/multitfa/branch/main/graph/badge.svg
:target: https://codecov.io/gh/biosustain/multitfa
:alt: Codecov
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/ambv/black
:alt: Code Style Black
.. image:: https://readthedocs.org/projects/multitfa/badge/?version=latest
:target: https://multitfa.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. summary-start
We present multiTFA, a multivariate thermodynamics-based metabolic flux analysis
package for Python. The framework takes advantage of the reactions' Gibbs free
energy covariance matrix to tightly constrain metabolic models using
thermodynamic constraints. It represents an improvement over a previous
thermodynamic metabolic flux analysis (tMFA) method described in [1]_.
This implementation requires a COBRA model as input, as well as additional
compartment conditions and metabolite concentrations. It allows user to perform
various thermodynamic analyses on COBRA models, such as thermodynamic metabolic
flux analysis, variability analysis, or flux sampling. Please see below for
further details.
Install
=======
To install multitfa from PyPI is as simple as: (We recommend using a `virtual environment `_).
.. code-block:: console
pip install multitfa
To install from source,
.. code-block:: console
git clone https://github.com/biosustain/multitfa.git
cd multitfa
pip install .
We highly recommend the installing `CPLEX `_. Although we support `GUROBI `_ solver, we noticed that it is slower and often stuck when solving quadratic constraint problems.
Please note, Installation takes upto 3 GB. This is to accomodate `equilibrator-api `_ database files.
Install Requirements
====================
Installation requires
- cobra
- depinfo
- optlang<1.4.6
- numpy
- scipy
- pandas
- equilibrator-api==0.3.2b7
- component-contribution==0.3.2b4
- equilibrator-cache==0.3.2b2
for testing purposes,
- pytest
- tox
An example test case was setup to get flux ranges of example script `paper_data_example.py` using `tox`. To run the test case, from inside `multitfa` directory
.. code-block:: console
pip install tox
tox -e examples
Usage
=====
The documentation is available online at `readthedocs `_.
Copyright
=========
* Copyright © 2018, Novo Nordisk Foundation Center for Biosustainability.
* Free software distributed under the `Apache Software License 2.0
`_.
Cite us
=======
If you use multitfa in a scientific publication, please cite `doi:10.1101/2020.12.01.407387 `_.
References
==========
.. [1] Henry, Christopher S., Linda J. Broadbelt, and Vassily Hatzimanikatis.
"Thermodynamics-Based Metabolic Flux Analysis."
*Biophysical Journal* 92, no. 5 (March 1, 2007): 1792–1805.
https://doi.org/10.1529/biophysj.106.093138.
.. [2] Vishnuvardhan Mahamkali, Tim McCubbin, Moritz Emanuel Beber, Esteban Marcellin, Lars Keld Nielsen.
"multiTFA: a Python package for multi-variate Thermodynamics-based Flux Analysis."
*bioRxiv* 2020.12.01.407387;
https://doi.org/10.1101/2020.12.01.407387
.. summary-end