This text is an introduction to dynamical modeling in computational cell biology. The target audience is students of biology, neuroscience, or mathematics at the advanced undergraduate or beginning graduate level. There are 4 editors and 17 contributors, but the treatment is much more uniform than might be expected because the core of the book is a set of course notes written by one person, the late Joel Keizer.
The book is divided into two major sections, an introductory course of 6 chapters covering the basic elements of compartmental modeling, and an additional section of 7 chapters covering divers advanced topics. Appendices contain details on mathematical and computational concepts. Topics discussed in the introductory course include voltage-gated ion currents, transporters and pumps, whole-cell calcium models, and intercellular communications. Advanced topics include diffusion in spatial modeling, modeling of calcium waves, biochemical oscillations, cell cycle controls, stochastic gating of ion channels, and molecular motors.
The text was designed to be independent of any particular software, but it would be difficult to do many of the exercises without employing the recommended XPPAUT package. XPPAUT solves ordinary differential equations and plots their solutions. It also incorporates numerical bifurcation software and methods for solving stochastic equations. XPPAUT is distributed without charge. However a significant amount of computer sophistication is required to dowload and apply it.