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A Python implementation of flux balance analysis

Project description

A python implementation of flux balance analysis to model microbial metabolism

About PyFBA

PyFBA is a Python flux-balance-analysis package that allows you to build models from genomes, gapfill models, and run flux-balance-analysis on that model. The aim of PyFBA is to provide an extensible, python-based platform for FBA work.

PyFBA is being developed by Daniel Cuevas, Taylor O’Connell, and Rob Edwards in Rob’s bioinformatics group at Flinders University, together with help from Janaka Edirisinghe, Chris Henry, Ross Overbeek and others at Argonne National Labs.

Installing PyFBA

We recommend that you install PyFBA using conda:

conda create -n pyfba -c bioconda pyfba

You can also install PyFBA from PyPi using pip and you will need Python 3 or greater, and you need to install the GNU GLPK and a Python wrapper for that program, pyGLPK available from GitHub.

Our installation page has detailed instructions on installing PyFBA and getting everything running.

Getting Started with PyFBA

Once you have installed GLPK, PyGLPK, and PyFBA, you will most likely want to build a model from a genome, gap fill that model, and test it for growth on different media. We have detailed instructions that walk you through the step-by-step procedures that you need to use to run flux balance analysis on your own genome.

Copyright and License

PyFBA is copyright Daniel Cuevas, Taylor O’Connell, and Rob Edwards, and is released under the MIT license.

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