2025/09/10 by Domenico Delli Gatti, Gatti, Domenico L.
Biochemistry, Genetics and Molecular Biology · #Cancer, Hypoxia, and Metabolism #FOS: Biological sciences #Metabolomics and Mass Spectrometry Studies #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN)
paper · pdf · doi:10.48550/arxiv.2509.08263
openalex publication_date 2025/09/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.