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Title: Automatic construction and simulation of Petri nets for a whole cell
P57
Hartmann, Kai; Schomburg, Dietmar

Kai.Hartmann@Uni-Koeln.De
University of Koeln, Institute for Biochemistry, Zuelpicher Str. 47, 50674 Koeln, Germany

Many efforts have been undertaken to model whole cells or parts of it. But only a few groups used Petri nets in the past. We developed two software tools. The first is used for automatic construction of a reaction-based Petri net for Design/CPN (www.daimi.au.dk/designCPN). All feasible reactions with corresponding enyzmes - if known- for a specific organism are needed as input data. The simulation is done by Design/CPN and analysed by the second software tool.

The first tool BuildNet maps each metabolite to one place and each reaction-enzyme-pair to one transition. If the reaction is reversible, a second transition is build. Transitions which represent the same enzyme are linked via a control place. Thus the concurrent firing of these transitions is disabled.

The second tool AnalyseSim analyses the complete simulation run. The variation of the marking of each place in selectable intervals and the number of firings of each transition in the progress of the simulation are evaluated. Large deviations are recorded as well as very small changes.

The tools were tested with a set of 597 reaction-enzyme-pairs from E. coli. Of these pairs, only the unique ones have been taken. This results in a set of 431 places (metabolites), 685 transitions (one-way reactions) and 2574 arcs. The results of the simulation runs are presented.

In addition to this approach, a new model has been build to allow regulative elements in the net. The introduction of regulation in dependency of the marking of just one place (ATP) leads to much better results. Currently the effect of more regulative elements and the introduction of standard Gibbs energies are being investigated.