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 …

Agent-based models (ABMs) have become an increasingly important mode of inquiry for the
life sciences. They are particularly valuable for systems that are not understood well enough …

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 …

Agent-based approaches to modelling biological phenomena are becoming popular and
proving successful in a number of areas. However, the underlying basis of these techniques …

Motivation: An increasing number of discrete mathematical models are being published in
Systems Biology, ranging from Boolean network models to logical models and Petri nets …

Background Many biological systems are modeled qualitatively with discrete models, such
as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to …

Highlights•Systems Biology Markup Language has greatly improved the dissemination of
many model types.•The representation of agent-based models (ABMs) remains in its infancy …

The use of models in biology is at once both familiar and arcane. It is familiar because, as
we shall argue, biologists presently and regularly use models as abstractions of reality …

Logical modelling and Petri nets constitute two complementary approaches for the
dynamical modelling of biological regulatory networks. Leaning on a translation of logical …

Models for systems biology commonly adopt Differential Equations or Agent-Based
modeling approaches for simulating the processes as a whole. Models based on differential …