XML Documentation of Biopathways and Their Simulations in Genomic Object Net

Hiroshi Matsuno [1] (matsuno@sci.yamaguchi-u.ac.jp)
Atsushi Doi [1] (atsushi@ib.sci.yamaguchi-u.ac.jp)
Yuichi Hirata [2] (hirata@ims.u-tokyo.ac.jp)
Satoru Miyano [2] (miyano@ims.u-tokyo.ac.jp)

[1] Faculty of Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan
[2] Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan


Abstract

Genomic Object Net is a software tool for modeling and simulating biopathways which employs the notion of hybrid functional net as its basic architechture. This paper shows how to integrate this basic architecture with XML documents for biopathway representations, simulations, and visualizations for creating a tailor-made simulation environment.

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Japanese Society for Bioinformatics