The tool Snoopy provides a unifying Petri net framework which has particularly many
application scenarios in systems and synthetic biology. The framework consists of two …

Owing to the availability of data of one biological phenomenon at different levels/scales,
modelling of biological systems is moving from single level/scale to multiple levels/scales …

We consider coloured Petri nets, qualitative and quantitative ones alike, as supported by our
PetriNuts tool family, comprising, among others, Snoopy, Marcie and Spike. Currently, most …

Membrane systems are a very powerful computational modelling formalism inspired by the
internal organisation of living cells. Modelling of membrane systems is challenged by …

In this paper we introduce a technique to encode spatial attributes of dynamic systems using
coloured Petri nets and show how it can be applied to biological systems within the spirit of …

Background Quorum sensing drives biofilm formation in bacteria in order to ensure that
biofilm formation only occurs when colonies are of a sufficient size and density. This spatial …

Modeling across multiple scales is a current challenge in Systems Biology, especially when
applied to multicellular organisms. In this paper, we present an approach to model at …

Petri nets have been widely used to model and analyze biochemical reaction networks. This
chapter gives an overview of different types of Petri nets within a unifying Petri net framework …

Coloured Petri nets are an excellent choice for exploring large biological models,
particularly when there are repetitions of components. Such models can be easily adapted …

Membrane systems are a very powerful computational modeling language inspired by the
internal organization of living cells. In this paper we explore the use of colored stochastic …