Modeling Biological Systems: Principles and Applications

This book is intended as a text for a first course on creating and analyzing computer simulation models of biological systems. The expected audience for this book are students wishing to use dynamic models to interpret real data mueh as they would use standard statistical techniques. It is meant to provide both the essential principles as well as the details and equa­ tions applicable to a few particular systems and subdisciplines. Biological systems, however, encompass a vast, diverse array of topics and problems. This book discusses only a select number of these that I have found to be useful and interesting to biologists just beginning their appreciation of computer simulation. The examples chosen span classical mathematical models of well-studied systems to state-of-the-art topics such as cellular automata and artificial life. I have stressed the relationship between the models and the biology over mathematical analysis in order to give the reader a sense that mathematical models really are useful to biologists. In this light, I have sought examples that address fundamental and, I think, interesting biological questions. Almost all of the models are directly COIIl­ pared to quantitative data to provide at least a partial demonstration that some biological models can accurately predict.

This extensively revised second edition of Modeling Biological Systems: Principles and Applications describes the essentials of creating and analyzing mathematical and computer simulation models for advanced undergraduates and graduate students. It offers a comprehensive understanding of the underlying principle, as well as details and equations applicable to a wide variety of biological systems and disciplines. Students will acquire from this text the tools necessary to produce their own models.

The text contains two major sections: Principles and Applications. The first section discusses the principles of biological systems with a thorough description of the essential modeling activities of formulation, implementation, validation, and analysis. These activities are illustrated by a set of example models taken from recent and classical literature, chosen for their breadth of coverage and current timeliness. The new edition updates extensively many of these topics, especially quantitative model formulation, validation and model discrimination using information theory measures and Bayesian probability, and stability analysis and non-dimensionalization.