This accessible text presents a detailed introduction to the use of a wide range of software tools and modeling environments for use in the biosciences, as well as the fundamental mathematical background. The practical constraints presented by each modeling technique are described in detail, enabling the researcher to determine which software package would be most useful for a particular problem.

Features include an introduction to a basic array of techniques to formulate models of biological systems and to solve them; discussions on agent-based models, stochastic modeling techniques, differential equations, spatial simulations, and Gillespie's stochastic simulation algorithm; exercises; descriptions of useful tools such as the Maxima algebra system, the PRISM model checker, and the modeling environments Repast Simphony and Smoldyn; and appendices on rules of differentiation and integration, and Maxima.