Welcome to the documentation for BOFdat

BOFdat is a package to generate biomass objective function stoichiometric coefficient (BOFsc) from experimental data. Often times the BOFsc used in genome-scale models (GEM) are simply fetched from another reconstruction work. This package is designed to help you stand out of the pack by using experimental data specific to your organism and increase the value of your model. The easiest way to use the BOFdat is to download via pip install (see install). A full usage example, reconstructing the BIOsc for Escherichia coli is available on GitHub. The entire source code is also available for developers.

Citing BOFdat

Please consider supporting BOFdat by citing our publication when you generate your BOFsc:


BOFdat can be installed using pip:

pip install BOFdat

include citation