A guide to biochemical systems modeling of sphingolipids for the biochemist.

The last several years have brought an avalanche of data from various high throughput, genome-wide analyses of yeast and other model organisms. Still, scientists struggle to comprehend the complex behavior of biological systems. One method that has been available for decades but now is more necessary than ever is the mathematical modeling of biological systems. Unfortunately, a chasm of terminology and techniques has separated most biologists from mathematical modelers. This chapter hopes to bridge that gap for metabolic models by delineating the general process used to develop a system of differential equations that describes a biochemical pathway. This modeling process can be generally applied to many biological phenomena. In addition, the specific approach of Biochemical Systems Theory (BST) is demonstrated for the nitty-gritty details of the model equations. These methods are demonstrated using the core section of ceramide metabolism in yeast.