RBAtools: a programming interface for Resource Balance Analysis models - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Bioinformatics Advances Year : 2023

RBAtools: a programming interface for Resource Balance Analysis models


Abstract Motivation Efficient resource allocation can contribute to an organism's fitness and can improve evolutionary success. Resource Balance Analysis (RBA) is a computational framework that models an organism's growth-optimal proteome configurations in various environments. RBA software enables the construction of RBA models on genome scale and the calculation of medium-specific, growth-optimal cell states including metabolic fluxes and the abundance of macromolecular machines. However, existing software lacks a simple programming interface for non-expert users, easy to use and interoperable with other software. Results The python package RBAtools provides convenient access to RBA models. As a flexible programming interface, it enables the implementation of custom workflows and the modification of existing genome-scale RBA models. Its high-level functions comprise simulation, model fitting, parameter screens, sensitivity analysis, variability analysis, and the construction of Pareto fronts. Models and data are represented as structured tables and can be exported to common data formats for fluxomics and proteomics visualization. Availability RBAtools documentation, installation instructions, and tutorials are available at https://sysbioinra.github.io/rbatools/. General information about RBA and related software can be found at rba.inrae.fr.
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Dates and versions

hal-04093676 , version 1 (10-05-2023)





Oliver Bodeit, Inès Ben Samir, Jonathan R Karr, Anne Goelzer, Wolfram Liebermeister. RBAtools: a programming interface for Resource Balance Analysis models. Bioinformatics Advances, 2023, pp.1-4. ⟨10.1093/bioadv/vbad056⟩. ⟨hal-04093676⟩
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