Computational Cell Biology - Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson.
This textbook provides an introduction to dynamic modeling in cell biology.
Access the VCell Models for Computational Cell Biology

Practical Kinetic Modeling of Large Scale Biological Systems - Robert Phair.
This online text steps you through the philosophy and practice of modeling, from the rationale for modeling to rate laws.

A Cell Biologist's Guide to Modeling and Bioinformatics. - Raquell Holmes.
This book contains a chapter with step by step discussion on creating a spatial calcium model originally published by Fink et. al., 2000. Release Dec. 21, 2007

VCell Tutorials

simple FRAP
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Facilitated Calcium Diffusion
Membrane Potential