Rule-based approaches (as in our own Kappa, or the BNG language, or many other
propositions allowing the consideration of" reaction classes'') offer new and more powerful …

The induction of a signaling pathway is characterized by transient complex formation and
mutual posttranslational modification of proteins. To faithfully capture this combinatorial …

We extend the notion of compositional associative rewriting as recently studied in the rule
algebra framework literature to the setting of rewriting rules with conditions. Our …

In this paper, we propose an abstract interpretation-based framework for reducing the state
space of stochastic semantics for protein protein interaction networks. Our approach consists …

This chapter aims to introduce some of the basics of modeling with ODEs in biology. We
focus on computational, numerical techniques, rather than on symbolic ones. We restrict our …

Modelling in biology becomes necessary when systems are complex. However, the more
complex the systems are, the harder models become to read and write. The most common …

We develop a novel method to analyze the dynamics of stochastic rewriting systems
evolving over finitary adhesive, extensive categories. Our formalism is based on the so …

Molecular biological models usually suffer from a large combinatorial explosion. Indeed,
proteins form complexes and modify each others, which leads to the formation of a huge …

One approach to modelling complex biological systems is to start from an abstract
representation of the biological process and then to incor-porate more details regarding its …

Computational simulation is a widely employed methodology to study the dynamic behavior
of complex systems. Although common approaches are based either on ordinary differential …