multitfa 0.1.2
Multivariate thermodynamics-based metabolic flux analysis in Python.
License: Apache-2.0
Requires Python: >=3.6
Keywords: thermodynamics,multivariate,flux analysis,metabolic,TMFA,TFA,multiTFA

========
multiTFA
========

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.. 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 <https://docs.python-guide.org/dev/virtualenvs/>`_).

.. 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 <https://www.ibm.com/analytics/cplex-optimizer>`_. Although we support `GUROBI <https://www.gurobi.com/>`_ 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 <https://gitlab.com/equilibrator/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

Usage
=====

The documentation is available online at `readthedocs <https://multitfa.readthedocs.io/en/latest/>`_.

Copyright
=========

* Copyright © 2018, Novo Nordisk Foundation Center for Biosustainability.
* Free software distributed under the `Apache Software License 2.0
  <https://www.apache.org/licenses/LICENSE-2.0>`_.


Cite us
=======

If you use multitfa in a scientific publication, please cite `doi:10.1101/2020.12.01.407387 <https://doi.org/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