Given the combinatorial nature of cellular signalling pathways, where biological agents can
bind and modify each other in a large number of ways, concurrent or agent-based …

Modelling is becoming a necessity in studying biological signalling pathways, because the
combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms …

The simulation of large systems of biochemical reactions is a key part of research into
molecular signaling and information processing in biological cells. However, it can be …

Cellular signalling pathways, where proteins can form complexes and undergo a large array
of post translational modifications are highly combinatorial systems sending and receiving …

We apply the multi-agent system (MAS) platform to the task of biological network simulation.
In this paper, we describe the simulation of signal transduction (ST) networks using the …

A grand challenge of computational systems biology is to create a molecular pathway model
of the whole cell. Current approaches involve merging smaller molecular pathway models' …

Motivation: Many important problems in cell biology require the dense nonlinear interactions
between functional modules to be considered. The importance of computer simulation in …

Agent-based modeling and simulation is a useful method to study biological phenomena in
a wide range of fields, from molecular biology to ecology. Since there is currently no agreed …

Rule-based modelling is particularly effective for handling the highly combinatorial aspects
of cellular signalling. The dynamics is described in terms of interactions between partial …

Recently, a collective effort from multiple research areas has been made to understand
biological systems at the system level. On the one hand, for instance, researchers working …