From quantitative SBML models to Boolean networks

Abstract Modelling complex biological systems is necessary for their study and understanding. Biomodels a repository of peer-reviewed models represented in the Systems Biology Markup Language (SBML). Most these are quantitative, but some cases, qualitative models—such as Boolean networks (BNs)—are better suited. This paper focuses on automatic transformation quantitative SBML to networks. We propose SBML2BN, pipeline dedicated this task. Our approach takes advantage several elements (reactions, rules, events) well numerical simulation concentration species over time constrain both structure dynamics synthesise. Finding all BNs complying with given was formalised an optimisation problem solved answer-set programming framework. run SBML2BN more than 200 models, we provide evidence that one can automatically construct which compatible model. In case model includes rules or events, also show how evaluation criteria impacted when taking into account.