Elements of Computational Systems Biology

9

INTEGRATING ABDUCTION AND INDUCTION IN BIOLOGICAL INFERENCE USING CF-INDUCTION

Yoshitaka Yamamoto

Department of Informatics, The Graduate University for Advanced Studies,Chiyoda-ku, Tokyo, Japan

Katsumi Inoue

Department of Informatics, The Graduate University for Advanced Studies,Chiyoda-ku, Tokyo, JapanNational Institute of Informatics, Chiyoda-ku, Tokyo, Japan

Andrei Doncescu

LAAS-CNRS, Avenue du Colonel Roche, Toulouse, France

9.1 INTRODUCTION

The newly emerging field of systems biology has been developed toward precise understanding of the whole mechanism of living cells and organisms. Metabolism is one of the essential biological systems oriented in this field. It is organized in a complex network of interconnected reactions, called a metabolic pathway [1], and its whole behavior results from individual properties of reactions and global properties of the network organization. An important key for understanding this whole metabolic system lies in regulatory mechanism on activities of enzymes catalyzing chemical reactions involved in metabolism. Metabolic flux analysis (MFA) [2, 3] is a methodology for quantitatively analyzing those enzymatic activities. The flux of a reaction, defined by the rate of the reaction, can be regarded as an effective value for indicating the activity of a certain enzyme catalyzing the reaction. There are two kinds of approaches for computing a flux distribution over the reactions. The first approach uses kinetics of chemical reactions and models ...