Modular assembly of cell systems biology models using P systems

Francisco J. Romero-Campero, Jamie Twycross, Miguel CáMara, Malcolm Bennett, Marian Gheorghe & Natalio Krasnogor

In this paper we propose an extension of a systems/synthetic biology modelling framework based on P systems that explicitly includes modularity. Modularisation in cellular systems can be produced by chemical specificity, spatial localisation and/or temporal modulation within cellular compartments. The first two of these modularisation features, the focus of this paper, can be easily specified and analysed in P systems using sets of rewriting rules to describe chemical specificity and membranes to represent spatial localisation. Our methodology enables the assembly of cell systems biology models by combining modules which represent functional subsystems. A case study consisting of a bacterial colony system is presented to illustrate our approach.

International Journal of Foundations of Computer Science 20 (03), 427-442