XML Pathway File Conversion between Genomic Object Net and SBML

Recently, the importance of biosimulation softwares in systems biology has been emphasized and received considerable attentions. Since the information conventionally created with most of biosimulation softwares does not have a common format for modeling, it has been very difficult to exchange pathway models among them. At present, the Systems Biology group of ERATO Kitano Symbiosis System Project takes the lead, and has proposed the standard language System Biology Mark-up Language (SBML) [1],which can give a common infrastructure for several biosimulation tools such as Bio/SPISE, E-Cell, DBSolve, Gepasi, Stochsim, and Virtual Cell. On the other hand, Genomic Object Net (GON) [2, 3] is a biosimulation system which uses hybrid functional Petri net (HFPN) and extensible markup language (XML) as basic mechanisms. With GON, even the researchers, who are not familiar with the mathematical modeling techniques such as differential equation and programming, can perform modeling and the simulation of a biological phenomenon easily. This paper compares XML description of GON with XML description of SBML, examines whether it could be converted from GON Assembler to SBML or vice versa, and investigates the automatic conversion between GON and SBML.