Bio-calculus: Its Concept and Molecular Interaction

Masao Nagasaki[1][2][3][5] (masao@ims.u-tokyo.ac.jp)
Shuichi Onami[1][5] (sonami@symbio.jst.go.jp)
Satoru Miyano[1][3] (miyano@ims.u-tokyo.ac.jp)
Hiroaki Kitano[1][4] (kitano@symbio.jst.go.jp)

[1] Systems Biology Group, Kitano Symbiotic Systems Project
ERATO, JST, M31 6A, 6-31-15, Jingu-Mae, Shibuya-ku, Tokyo 150-0001, Japan
[2] Department of Information Science, University of Tokyo
7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0034, Japan
[3] Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
[4] Sony Computer Science Laboratory
3-14-13 Higashi-Gotanda, Shinagawa, Tokyo 141 Japan
[5] These authors equally contributed to this paper.


Abstract

The way for expressing biological systems is a key element of usability. Expressions used in the biological society and those in the computer science society have their own merits. But they are too different for one society to utilize the expressions of the other society. In this paper, we design the bio-calculus that attempts to bridge this gap. We provide syntax which is similar to conventional expressions in biology and at the same time specifies information needed for simulation analysis. The information and mathematical background of bio-calculus is what is desired for the field of computer science. We show the practicality of bio-calculus by describing and simulating some molecular interactions with bio-calculus.

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Japanese Society for Bioinformatics