An introduction to kinetic, constraint-based and Boolean modeling in systems biology

Abstract

Mathematical modeling and model analysis of biochemical reaction networks are becoming important tools for biological research and for applications in medicine and bioprocess engineering. We will discuss the special role of mathematical modeling in biological research. In engineering applications, models are primarily means to accomplish a design task (e.g. controller design). In contrast, the goal of modeling in biology is often to coherently and comprehensively integrate and develop the knowledge of a biological system beyond the level of the conventional verbal or graphical descriptions. In this way, modeling supports biologists in exploring biochemical networks. This tutorial gives an overview over several available modeling techniques with respect to their area of application: Kinetic modeling provides a detailed, dynamic and quantitative model of cellular reaction networks. Constraint-based modeling is applicable to large metabolic networks and Boolean modeling is applicable to large signal transducing networks. This tutorial paper addresses researchers with an engineering background that start to make themselves familiar with modeling in systems biology.