Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

TL;DR

This paper introduces a modeling framework combining Petri nets and topological collections to analyze regulation processes in multi-cellular biological systems, enabling spatial and regulatory analysis with exhaustive state exploration.

Contribution

It presents a novel integration of Petri nets with topological collections for spatial regulation modeling in multi-cellular systems, along with a prototype implementation.

Findings

Framework supports exhaustive state space exploration.

Prototype demonstrates applicability to biological tissue regulation.

Combines logical regulatory networks with spatial information.

Abstract

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.