Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Petri net modelling of biological regulatory networks
Journal of Discrete Algorithms
Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
Compositional Definitions of Minimal Flows in Petri Nets
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Case for Using Signal Transition Graphs for Analysing and Refining Genetic Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
Stochastic Petri net models of Ca2+ signaling complexes and their analysis
Natural Computing: an international journal
Petri net models for the semi-automatic construction of large scale biological networks
Natural Computing: an international journal
Neural system modeling and simulation using hybrid functional Petri net
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Survey: Computational challenges in systems biology
Computer Science Review
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Motivation: New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. Results: We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non--determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. Availability: The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn Contact: L.J.Steggles@ncl.ac.uk