Information Visualization and Visual Data Mining
IEEE Transactions on Visualization and Computer Graphics
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Proceedings of the 35th conference on Winter simulation: driving innovation
SimWiz3D - Visualising Biochemical Simulation Results
MEDIVIS '05 Proceedings of the Third International Conference on Medical Information Visualisation--BioMedical Visualisation
Petri Net Based Descriptions for Systematic Understanding of Biological Pathways
IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences
Towards biopathway modeling and simulation
ICATPN'03 Proceedings of the 24th international conference on Applications and theory of Petri nets
Discrete, Continuous, and Hybrid Petri Nets
Discrete, Continuous, and Hybrid Petri Nets
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The large quantity of data generated by the simulation of complex biochemical models is difficult to interpret with traditional plots of time series data. A visualization method has been developed and software tools have been implemented. They are efficient with models of metabolic networks in which molecules are produced, consumed and degraded. However, models of signaling pathways in which enzymes are either activated or deactivated to transmit a signal are not handled well with the existing method. In this paper, we present a new visualization method using the painted feature of Petri nets and their invariant properties. We apply the first steps of this method to the continuous Petri net model of the calmodulin pathway. We also present the methodology that we will use to compare the existing visualization method with our Petri net-based method and to verify if it is more suited for signaling pathways.