Biopathway Model Conversion from E-CELL to Genomic Object Net

E-CELL [3] is a cenceputually attractive biosimulation tool for representing and simulating biopathways. With E-CELL, Tomita et al. [4] have modeled several biopathways including biochemical reactions in human erythrocyte, signal transduction for bacterial chemotaxis, energy metabolism in mitochondria and lytic-lysogenic switch network of λ phage. On the other hand, we developed a tool for representing and simulating biopathways called “Genomic Object Net (GON) Assembler” which uses hybrid functional Petri net (HFPN) as a basic mechanism for representing biopathways [1] where XML documentation of biopathways and their simulatons is also realized as another tool in Genomic Object Net [2]. The purpose of this paper is to show a procedure for converting biopathway models with E-CELL to the ones executable on GON Assembler. Thus E-CELL can be regarded as a subset of Genomic Object Net. A conversion program of E-CELL to GON Assembler is being developed.