KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models

Tools paper trackInternational audienceKappa is a formal language that can be used to model sys- tems of biochemical interactions among proteins. It offers several se- mantics to describe the behaviour of Kappa models at different levels of abstraction. Each Kappa model is a set of context-free rewrite rules. One way to understand the semantics of a Kappa model is to read its rules as an implicit description of a (potentially infinite) reaction net- work. KaDE is interpreting this definition to compile Kappa models into reaction networks (or equivalently into sets of ordinary differential equations). KaDE uses a static analysis that identifies pairs of sites that are indistinguishable from the rules point of view, to infer backward and forward bisimulations, hence reducing the size of the underlying reaction networks without having to generate them explicitly. In this paper, we describe the main current functionalities of KaDE and we give some benchmarks on case studies

Using alternated sums to express the occurrence number of extended patterns in site-graphs

To appearInternational audienceSite-graph rewriting languages as Kappa or BNGL supply a convenient way to describe models of signalling pathways. Unlike classical reaction networks, they emphasise on the biochemical structure of proteins. We use patterns to formalise properties about bio-molecular species. Intentionally, a pattern is a part of a species, but extensionally it denotes the multi-set of the species containing this pattern (with the multiplicity). Thus reasoning on patterns allows to handle symbolically arbitrarily big (if not infinite) multi-sets of species. This is a key point to design fast simulation algorithms or model reduction schemes. In this paper, we introduce the notion of extended patterns. Each extended pattern is made of a classical pattern and of a set of potential bonds between pairs of sites. Extended patterns have positive (when at least one of the potential bonds is realised) and negative (when none is realised) instances. They are important to express the consumption and the production of patterns by the rules that may break cycles in bio-molecular species by side-effects. We show that the number of positive (resp. negative) instances of extended patterns may be expressed as alternated sums of the number of occurrences of classical patterns

Programming Languages and Systems

This open access book constitutes the proceedings of the 28th European Symposium on Programming, ESOP 2019, which took place in Prague, Czech Republic, in April 2019, held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2019

Incremental Update for Graph Rewriting

International audienc

Incremental Update for Graph Rewriting

International audienc