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Integration of external biomass reactions into existing metabolic models

María Moscardó García, View ORCID ProfileMaria Pacheco, View ORCID ProfileThomas Sauter
doi: https://doi.org/10.1101/2022.08.01.502323
María Moscardó García
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, 4367, Belvaux, Luxembourg
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Maria Pacheco
2Department of Life Sciences and Medicine, University of Luxembourg, 6 avenue du Swing, 4367, Belvaux, Luxembourg
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Thomas Sauter
2Department of Life Sciences and Medicine, University of Luxembourg, 6 avenue du Swing, 4367, Belvaux, Luxembourg
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  • For correspondence: thomas.sauter@uni.lu
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Summary

Currently, seven biomass objective functions have been defined in human metabolic reconstructions. The integration of published biomass reactions into alternative models can contribute to the prediction power of the model. Thus, in this work, we present a workflow to integrate reactions and biomass functions originating from several genome-scale reconstructions into models other than their home models. Additionally, a benchmark to identify the biomass that confers the highest prediction accuracy in terms of gene essentiality and growth predictions is provided.

For complete details on the use and execution of this protocol, please refer to Moscardó García et al. (2021).

Competing Interest Statement

The authors have declared no competing interest.

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Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted August 03, 2022.
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Integration of external biomass reactions into existing metabolic models
María Moscardó García, Maria Pacheco, Thomas Sauter
bioRxiv 2022.08.01.502323; doi: https://doi.org/10.1101/2022.08.01.502323
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Integration of external biomass reactions into existing metabolic models
María Moscardó García, Maria Pacheco, Thomas Sauter
bioRxiv 2022.08.01.502323; doi: https://doi.org/10.1101/2022.08.01.502323

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