Applying Petri Nets to Systems Biology using XML Technologies (2004)

Author(s): Shaw O, Koelmans A, Steggles J, Wipat A

    Abstract: Systems Biology is a rapidly developing discipline which utilises mathematical and computer science techniques to analyse and interpret biological models. Petri nets have been proposed as an effective formalism for Systems Biology but so far only a small number of simple manual Petri net models have been constructed and investigated. In this paper we present a scheme for automatically mapping biological systems into Petri net models using XML technology. We develop a simple prototype tool which translates Systems Biology Markup Language (SBML) to the Petri Net Markup Language (PNML). As an illustrative example we consider mapping a SBML description of the Saccharomyces cerevisiae glycolysis pathway into PNML. An analysis of the resulting PNML model then demonstrates that even basic invariant analysis can produce interesting results for biologists. Finally we discuss what features may be desirable to systems biologists in future modifications of the PNML standard.

      • Date: March 2004
      • Series Title: School of Computing Science Technical Report Series
      • Pages: 38
      • Institution: School of Computing Science, University of Newcastle upon Tyne
      • Publication type: Report
      • Bibliographic status: Published

      Keywords: Petri ntes, XML, bioinformatics, Systems Biology, SBML, PNML


      Professor Anil Wipat
      Professor of Integrative Bioinformatics