Visualization of the simulation data of biochemical network models: a painted Petri net approach
Proceedings of the 2007 Summer Computer Simulation Conference
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Proceedings of the 3rd International Conference on Bio-Inspired Models of Network, Information and Computing Sytems
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
Stochastic Petri net models of Ca2+ signaling complexes and their analysis
Natural Computing: an international journal
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Biomodel engineering – from structure to behavior
Transactions on Computational Systems Biology XII
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Petri nets have recently become widely accepted as a description method for biological pathways by researchers in computer science as well as those in biology. This paper gives an overview of Petri net formalisms to describe biological pathways and discusses their use in modelings and simulations for the systematic understandings of biological pathways. After reviewing the use of various types of Petri nets for the biological pathway modelings, we showed the examples that analyze fundamental properties of biological pathways using T-invariant, P-invariant, siphon, and trap. Applications of hybrid Petri nets for producing new biological hypotheses through simulations are also illustrated.