A simple method to extend COBRApy dynamic FBA protocol to the metabolic simulation of communities

Domenico L. Gatti

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arXiv · 2509.08263

A simple method to extend COBRApy dynamic FBA protocol to the metabolic simulation of communities

Domenico L. Gatti

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Abstract

Dynamic Flux Balance Analysis (dFBA) extends the capabilities of FBA to track changes in metabolite concentrations and fluxes over time in response to environmental conditions and cellular processes. The key idea of the method called dynamic parallel FBA (dpFBA) is to assign each species to a separate compartment, and to perform dFBA on the individual compartments while keeping track of the shared pool of external metabolites at each time interval. The software package COBRApy for Constraint-Based Modelling currently offers only an out-of-the-box dFBA implementation for the simulation of the batch growth of a single species over an interval divided in $n$ time steps. Here we describe a simple method to extend COBRApy dFBA to a community of species, by implementing dpFBA without any modification of the current package.

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Domenico L. Gatti. 2025-09-10. A simple method to extend COBRApy dynamic FBA protocol to the metabolic simulation of communities. https://arxiv.org/abs/2509.08263

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