Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding

International audience; Boolean modelling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. This is even more true for very large models where such data is frequently missing and led to a constant increase in size of logical models à la Thomas. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes. The recent use of trap spaces made a real breakthrough in that field allowing to consider medium-sized models that used to be out of reach. However, with the continuing increase in model-size, the state-of-the-art computation of minimal trap spaces based on prime-implicants shows its limits as there can be a huge number of implicants.In this article we present an alternative method to compute minimal trap spaces, and hence complex attractors, of a Boolean model. It replaces the need for prime-implicants by a completely different technique, namely the enumeration of maximal siphons in the Petri net encoding of the original model. After some technical preliminaries, we expose the concrete need for such a method and detail its implementation using Answer Set Programming. We then demonstrate its efficiency and compare it to implicant-based methods on some large Boolean models from the literature.