Qualitative reasoning: modeling and simulation with incomplete knowledge
Qualitative reasoning: modeling and simulation with incomplete knowledge
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Self-Modifying Nets, a Natural Extension of Petri Nets
Proceedings of the Fifth Colloquium on Automata, Languages and Programming
Visualization of the simulation data of biochemical network models: a painted Petri net approach
Proceedings of the 2007 Summer Computer Simulation Conference
Hybrid simulation of biochemical systems using hybrid adaptive Petri nets
Proceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools
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
Target driven biochemical network reconstruction based on petri nets and simulated annealing
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
Hybrid Petri net based modeling for biological pathway simulation
Natural Computing: an international journal
From petri nets to differential equations – an integrative approach for biochemical network analysis
ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
Discrete event multi-level models for systems biology
Transactions on Computational Systems Biology I
Modelling a biological system: network creation by triplet extraction from biological literature
Bisociative Knowledge Discovery
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Petri net has been employed for modeling metabolic pathways as well as signal transduction pathways and gene regulatory networks. The purpose of this paper is to introduce an extension of Petri net called hybrid functional Petri net (HFPN) which allows us to model biopathways naturally and effectively. The method for creating biopathways with HFPN is demonstrated through a well-known biopathway example "lac operon gene regulatory mechanism and glycolytic pathway." In order to evaluate this biopathway model, simulations of five mutants of the lac operon are carried out by Genomic Object Net which is a biopathway simulator based on the HFPN architecture. The software Genomic Object Net and the HFPN files presented in this paper can be downloaded from http://www.GenomicObject.Net/.