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bioRxiv · 10.1101/243881

BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

Lachance, J.-C.·Monk, J. M.·Lloyd, C. J.·Seif, Y.·Palsson, B. O.·Rodrigue, S.·Feist, A. M.·King, Z. A.·Jacques, P.-E.
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Abstract

Genome-scale models (GEMs) rely on a biomass objective function (BOF) to predict phenotype from genotype. Here we present BOFdat, a Python package that offers functions to generate biomass objective function stoichiometric coefficients (BOFsc) from macromolecular cell composition and relative abundances of macromolecules obtained from omic datasets. Growth-associated and non-growth associated maintenance (GAM and NGAM) costs can also be calculated by BOFdat.\n\nBOFdat is freely available on the Python Package Index (pip install BOFdat). The source code and an example usage (Jupyter Notebook and example files) are available on GitHub (https://github.com/jclachance/BOFdat). The documentation and API are available through ReadTheDocs (https://bofdat.readthedocs.io).\n\nContactjean-christophe.lachance@usherbrooke.ca, zaking@eng.ucsd.edu, pierre-etienne.jacques@usherbrooke.ca

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Lachance, J.-C., Monk, J. M., Lloyd, C. J., Seif, Y., Palsson, B. O., Rodrigue, S., Feist, A. M., King, Z. A., Jacques, P.-E.. 2018-01-05. BOFdat: generating biomass objective function stoichiometric coefficients from experimental data. https://doi.org/10.1101/243881

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