ABSTRACT
This chapter focuses on the workhorse of computational systems biology: sets of ordinary differential equations (ODEs) based on conservation of mass and mass action kinetics. Systems of ODEs have been used for all kinds of applications. The chapter provides a comparison between various systems based on key equation parameters, such as steady-state solution, step response, and response time. It explains how solve ODEs analytically. For example, ODEs not much more complicated than our rain gutter example have been used to model the spread of human immunodeficiency virus from cell to cell and from person to person, leading to recommendations that had an impact on health policy. The most common approach for describing models of biological systems is to write a set of ODEs. A convenient way to conceptualize ODEs is to draw a compartment model diagram, which shows the variables as blocks; the processes that change the variable values are given as arrows pointing toward or away from the blocks.
