Bioinformatics pathway modeling

J. V. Rodriguez, J. A. Kaandorp, M. Dobrzynski, and J. K. Blom, Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli, Bioinformatics 22, 1895 (2006). 

I. Koch, B. H. Junker, and M. Heiner. Application of Petri net theory for modeling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7), 1219 1226 (2005). 

Metabolic pathways have been illustrated using simple diagrams since before the human genome project and related bioinformatics projects had begun. With the involvement of computer science techniques, however, systematic approaches to modeling metabolic pathways have progressed quickly, with various aims that range from metabolite analyses to pathway prediction and reconstruction (1-3). Systems analysis has come to incorporate... 

The Protein Function and Biochemical Pathways project, and its aMAZE database [van Helden 2000] are an ongoing effort since 1998 under the leadership of Shoshana Wodak of the European Bioinformatics Institute and the Free University of Brussels. It includes an encompassing object-oriented data model and has begun development of pathway visualization and analysis tools. 

Deville, Y., D. Gilbert, J. van Helden, and S. J. Wodak. 2003. An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4 246-59. 

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