Development of Genomic Object Net Builder for Supporting XML Design for Visualization

Genomic Object Net (GON) is a biosimlation tool that allows us to model various kinds of biopathways including gene regulatory networks, metabolic pathways, and signal transduction pathways in a biologically intuitive way [4]. In GON, biopathway is modeled as an extension of hybrid Petri net called hybrid functional Petri net (HFPN) for which XML documentation is defined. As a graphical editor of a biopathway, GON equips with a tool GON Assembler for drawing and simulating the biopathway. Of couse, user need not touch any XML definitions. Furthermore, neither ordinary differential equations with messy coefficients nor programming labors are explicity required for user to model biopathways in GON. Since it is designed so powerful and flexible, E-CELL can also be realized as a subsystem of GON [1]. GON also has a visulalization tool for simulation called GON Visualizer. By writing an XML document for GON Visualizer, user can animate and see visually the interactions in a biopathway so that user can create and test hypotheses for biological phenomena [2, 3]. However, user has to write XML documents for personalized visualization although it is not a disastrous obstacle like the ODE designs and C++ programming for biologists.