Systems biology has been brought to the forefront of life-science-based research and development. The need for systems analysis is made apparent by the inability of focused studies to explain whole network, cell, or organism behavior, and the availability of component data is what is fueling and enabling the effort. This massive amount of experimental information is a reflection of the complex molecular networks that underlie cellular functions. Reconstructed networks represent a common denominator in systems biology. They are used for data interpretation, comparing organism capabilities, and as the basis for computing their functional states. The companion book [89] details the topological features and assessment of functional states of biochemical reaction networks and how these features are represented by the stoichiometric matrix. In this book, we turn our attention to the kinetic properties of the reactions that make up a network. We will focus on the formulation of dynamic simulators and how they are used to generate and study the dynamic states of biological networks.

Biological networks

Cells are made up of many chemical constituents that interact to form networks. Networks are fundamentally comprised of nodes (the compounds) and the links (chemical transformations) between them. The networks take on functional states that we wish to compute, and it is these physiological states that we observe. This text is focused on dynamic states of networks.

There are many different kinds of biological network of interest, and they can be defined in different ways.