Genomic Object Net: I. A platform for modelling and simulating biopathways.
Genomic Object Net (GON) 1.0 is a software package for creating models and simulations of biopathways. Its core architecture employs the notion of a hybrid functional Petri net with extension (HFPNe). HFPNe can seamlessly handle discrete and continuous objects and events while keeping the model components themselves simple. With the feature and graphical model editor, biopathways can be modelled intuitively and simulated on GON. The subsequent output of the simulation results can be evaluated in customised views on GON Visualizer by writing an XML file. Additionally, GON provides a tool to transform biopathway models in KEGG and BioCyc to the GON XML files for modelling and simulation. The tool avoids a lot of tedious work by users, enabling them to focus on the biological model.
Nagasaki
Masao
M
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan. masao@ims.u-tokyo.ac.jp
Doi
Atsushi
A
Matsuno
Hiroshi
H
Miyano
Satoru
S
D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D004282:Documentation; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D009097:Multienzyme Complexes / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
D009097:Multienzyme Complexes