ABSTRACT
This chapter presents mathematical and computational methods for analyzing dynamic systems. It formalizes concepts of model design, diagnostics, and analysis in more depth and provides the skills to set up and analyze models from scratch. In contrast to a typical math book, which uses the famous lemma–theorem–proof–corollary–example style, the chapter introduces concepts and definitions on the fly, uses examples as motivation, and stops before things get too complicated. In particular, the entire field of linear algebra addresses the systems and has developed concepts such as vectors and matrices that have become absolutely fundamental throughout mathematics and computer science. Most biological systems are too complicated to be describable by explicit functions, and even ordinary differential equation models are not always sufficient. In a biological context, such an alteration could represent a mutation or some permanent change in an enzyme activity that could be due to aging or disease.
