multitfa 0.1.0

Multivariate thermodynamics-based metabolic flux analysis in Python.

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.

[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.

Install

It’s as simple as:

pip install multitfa

We highly recommend the installation of a commercial mathematical optimization solver, like GUROBI or CPLEX.

Usage

Please take a look at the Python scripts and Jupyter notebooks in the examples directory.

Copyright

• Copyright © 2018, Novo Nordisk Foundation Center for Biosustainability.

• Free software distributed under the Apache Software License 2.0.