Elements of Computational Systems Biology

6

SIMULATING FILAMENT DYNAMICS IN CELLULAR SYSTEMS

Wilbur E. Channels and Pablo A. Iglesias

Department of Electrical and Computer Engineering,The Johns Hopkins University, Baltimore, MD, USA

6.1 INTRODUCTION

Increasingly, there is an appreciation of the importance of computational models in biology. These models of biological systems have principally been used to show the level of quantitative understanding of the systems in terms of how well they produce previously observed behavior or more importantly produce a “testable hypothesis relevant to important problems” [1].

Computational models provide two significant benefits. First, they help to test conceptual models of how signaling networks interact. This is particularly important when the number of interacting components is large or when the network topology is complex—for example, containing numerous feedback loops or cross-talk between different pathways. Second, computational models provide testable hypotheses that can lead to new insight into the function of biological systems.

Most computational models in biology are based on ordinary differential equation implementations of molecular wiring diagrams [2]. The states that are updated by these equations represent the concentrations of biochemical species. Standard techniques are then used to translate the nature of the interactions (e.g., Michaelis–Menten kinetics to describe enzymatic reactions) into the correct equations. As the scope of systems being modeled increases from ...