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bioRxiv · 10.1101/2021.05.20.445041

MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox

Griesemer, M.·Navid, A.
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Abstract

Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs), Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software package for conducting a plethora of different types of constraint-based analyses using GSMs is the COBRA Toolbox for MATLAB. We have developed a new add-on tool for this toolbox using Normalized Normal Constraint (NNC) that performs MOFA for a number of objectives only limited by computation power (n [≤] 10). This development will facilitate MOFA analyses by COBRAs large user base and allow greater multi-faceted examination of metabolic trade-offs in complicated biological systems. Availability and ImplementationThe MOFA software is freely available for download from https://bbs.llnl.gov under the GPL v2 license. The program runs on MATLAB with the COBRA software on Windows, Linux, and MacOS. It includes a detailed manual explaining the input and output of a simulation, a listing of the codes functions, and an example MOFA run using a well-curated GSM model of E. coli. Contactgriesemer1@llnl.gov or navid1@llnl.gov

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Griesemer, M., Navid, A.. 2021-05-22. MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox. https://doi.org/10.1101/2021.05.20.445041

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