Nagasaki, Masao;Doi, Atsushi;Sasaki, Makiko;Savoie, Christopher J.;Matsuno, Hiroshi;Miyano, Satoru - Genomic Object Net in JAVA: A Platform for Biopathway Modeling and Simulation

ECCB 2002 Poster sorted by: Author | Number

Next | Previous poster (in order of the view you have selected)

Title: Genomic Object Net in JAVA: A Platform for Biopathway Modeling and Simulation	P112
Nagasaki, Masao; Doi, Atsushi; Sasaki, Makiko; Savoie, Christopher J.; Matsuno, Hiroshi; Miyano, Satoru masao@ims.u-tokyo.ac.jp, Matsuno@sci.yamaguchi-u.ac.jp Human Genome Center, Institute of Medical Science, University of Tokyo

In the post-genome era, biopathway information processing will be one of the most important issues in Bioinformatics. Development of Genomic Object Net [1] is our approach to this issue. This software aims at describing and simulating structurally complex dynamic causal interactions and processes such as metabolic pathways, signal transduction cascades, gene regulations. We have released Genomic Object Net (ver. 0.919) in 2001. With this system, we have shown that we can reorganize and represent various biopathway information so that biopathways can be modeled and simulated for new hypothesis generation and testing (see [1, 2, 3]).
Although we have succeeded in modeling and simulating various biopathways without so much efforts, we have further identified more inconveniences through our biopathway modeling activities. This motivated us to develop a new version Genomic Object Net in JAVA (ver. 1.0) (JAVA GON for short) from scratch. Figure 1 is an screen shot of JAVA GON which shows the simulation of apoptosis induced by Fas protein. It inherits basic ideas and concepts in Genomic Object Net (ver. 0.919) while enhancing the ability for handling not only biopathways but also localization information and multicellular processes.
As its basic architecture, Genomic Object Net employs the notion of hybrid functional Petri net (HFPN) that is a newly defined notion obtained by extending hybrid Petri net [4] and hybrid object net [5] so that various aspects in biopathways can be smoothly modeled while inheriting good traditions from the research on Petri net. In HFPN, hybrid system of continuous and discrete events with functional enhancement for transitions is very suited for modeling various interactions and reactions, and the hierarchization of objects provides diversity in intuitive creation of complex objects. Furthermore, we have extended the HFPN architechture by allowing more ``types'' for data (integer, real, boolean, string) with which more complex information such as localization, multicellular process, etc. can be handled smoothly. Genomic Object Net represents the objects in a biopathway as places and the biopathway as a network comprising of transitions among objects. Although Petri net has been studied independently of biology, its affinity to biopathways is surprisingly good. Such enhancement to Petri net changed it to an excellent architecture for biopathway modeling and simulation.
In JAVA GON, a biopathway is represented as an extended HFPN which is described as an XML document. We have also provided a package for XML with which we can design a personalized visualization environment for simulation [3]. In Figure 1, visualization of the simulation result of apoptosis with this package is displayed. This XML based personalized visualization environment for simulation result evaluaton is very helpful in tuning parameters in models. This environment will provide a more creative biopathway modeling which may not be achieved only with time-course graph representation. Furthermore, a GUI is developed for realizing more biological intuitions and ``thinking'' when we design HFPNs. We shall show some modelings and simulations of biopathways with JAVA GON. With this new implementation, JAVA GON runs on Linux, MacOS, Unix while the former version runs only on Windows 2000/Me/XP.

[1] http://www.GenomicObject.Net/
[2] Matsuno, H., Doi, A., Nagasaki, M., Miyano, S. (2000). Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing 5, 338-349.
[3] Matsuno, H., Doi, A., Hirata, H., Miyano, S. (2001). XML documentation of biopathways and their simulations in Genomic Object Net. Genome Informatics 12, 54-62.
[4] Alla, H., David, R. (1998). Continuous and hybrid Petri nets. J. Circuits, Systems, and Computers 8 (1), 159-188.
[5] Drath, R. (1998). Hybrid object nets: An object oriented concept for modeling complex hybrid systems. Proc. Hybrid Dynamical Systems, 3rd Intern. Conf. on Automation of Mixed Processes, ADPM'98, 437-442.