RESEARCH ARTICLE

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes

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  • 1. Shanghai Center for Bioinformation Technology, Shanghai 200235, China; 2. College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; 3. Shanghai Jiaotong University School of Medicine, Shanghai 200025, China

Received date: 21 Dec 2011

Accepted date: 04 Feb 2012

Published date: 01 Mar 2012

Abstract

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

Cite this article

Junhui Gao, Li Li, Xiaolin Wu, Dong-Qing Wei . BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes[J]. Protein & Cell, 2012 , 3(3) : 225 -229 . DOI: 10.1007/s13238-012-2019-4

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