https://github.com/linsalrob/pyfba

A python implementation of flux balance analysis to model microbial metabolism
https://github.com/linsalrob/pyfba

Last synced: over 1 year ago
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A python implementation of flux balance analysis to model microbial metabolism

• Host: GitHub
• URL: https://github.com/linsalrob/pyfba
• Owner: linsalrob
• License: mit
• Created: 2015-11-15T23:51:34.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2023-02-25T21:54:29.000Z (over 3 years ago)
• Last Synced: 2024-10-10T09:35:04.424Z (over 1 year ago)
• Language: Python
• Homepage: http://linsalrob.github.io/PyFBA/
• Size: 11.3 MB
• Stars: 25
• Watchers: 6
• Forks: 14
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.md
  • License: LICENSE
  • Citation: CITATION.md

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README

          
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# PyFBA

A python implementation of flux balance analysis to model microbial metabolism. [Read more ...](http://linsalrob.github.io/PyFBA/)

## 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](http://edwards.flinders.edu.au/) initially at [San Diego State University](http://www.sdsu.edu/) and now at 

[Flinders University](http://www.flinders.edu.au/). 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](http://www.theseed.org/).

You can [read more about PyFBA](http://linsalrob.github.io/PyFBA/) on our github.io pages.

## Installing PyFBA

PyFBA is available in [bioconda](https://bioconda.github.io/) and we recommend installing it that way. It's what we 

use!

```commandline

conda create -n pyfba -c bioconda pyfba

conda activate pyfba

pyfba -v

pyfba help

```

There are other options described in the [installation documents](INSTALLATION.md), 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](GETTING_STARTED.md) 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:

```commandline

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.