A Tool for Using the SBML Format to Represent P Systems which Model Biological Reaction Networks

Abstract

In this paper we present a software tool to represent P systems modelling signalling networks of biochemical reactions using SBML (Systems Biology Markup Language), a machine-readable format for describing qualitative and quantitative models of biochemical networks. CLIPS (C Language Integrated Production System), a tool which provides a complete environment for the construction of rule and/or object based expert systems, has been used to simulated membrane system. Our tool acts as a translator from SBML to CLIPS; that is, besides providing an environment for writing SBML code it also parses this code and generates automatically the CLIPS code that simulates the membrane system represented in SBML.