PyFBA

A python implementation of flux balance analysis to model microbial metabolism. Read more ...

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 initially at San Diego State University and now at Flinders University. Amazing help was also provided by the developers of the ModelSEED, in particular Janaka Edirisinghe, Chris Henry, Ross Overbeek and others at Argonne National Labs.

You can read more about PyFBA on our github.io pages.

Installing PyFBA

PyFBA is available in bioconda and we recommend installing it that way. It's what we use!

conda create -n pyfba -c bioconda pyfba
conda activate pyfba
pyfba -v
pyfba help

There are other options described in the installation documents, but just use conda!

Getting Started with PyFBA

Once you have installed 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.

Citing PyFBA

Please use the command:

pyfba citations

to get the citations for PyFBA. They are available in plain text and bibtex format, please let us know if you would like other formats!

Copyright and License

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