rbatools -a programming interface to cellular resource allocation modelling with Resource Balance Analysis | rbatools
2021
Bodeit, Oliver | Liebermeister, Wolfram | Goelzer, Anne | Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
International audience
Afficher plus [+] Moins [-]anglais. rbatools has been developed as a programminginterface around RBApy2, facilitating the flexibleimplementation of analyses on cellular resourceallocation, beyond the representation of growth-optimal cellular configurations. The tool utilisesthe flexible formulation of RBA, as constraint-based linear problem, to alter and extend themodel’s scope and structure by the addition andmodification of user-defined constraints oncellular growth and maintenance. The internalmodel representation database allows to accessinformation on model structure and components,complemented with external annotations, and toexport this information to tabular formats (SBtabor CSV). Fundamental methods allow toprogramatically vary model parameters, setenvironmental conditions such as medium-composition and growth rate, define cellularobjectives, solve the specific RBA problem andexport simulation results to various formats (e.gSBtab, JSON or CSV and inputs to Escher- andProteomaps for visualisation). Implementedalgorithms include finding the environment-specific optimal growth rate, specific feasibleranges of model variables, applying and evaluatingthe effect of gene knock-outs. Exemplaryapplications (results to the right) were obtainedwith an existing E. coli RBA model2, during thedevelopment process.
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