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

作　　者：Junhui Gao Li Li Xiaolin Wu Dong-Qing Wei 

机构地区：[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

出　　处：《Protein & Cell》2012年第3期225-229,共5页蛋白质与细胞（英文版）

基　　金：supported by grants from the National Basic Research Program of China(973 Program)(Grant No.2012CB721000);the Key Project of Shanghai Science and Technology Commission(No.11JC1406400);the Research Innovation Project of Shanghai Education Commission(No.09YZ95).

摘　　要：BioNetSim,a Petri net-based software for modeling and simulating biochemistry processes,is developed,whose design and implement are presented in this pa-per,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.

关 键 词：biochemical processes simulation soft-ware Petri net Gillespie 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]