Improving the development process for eukaryotic cell cycle models with a modeling support environment

Biological pathway modelers attempt to describe cellular processes and regulatory networks with continuous and discrete models of the cell cycle. Previous practice has been to develop these models largely by hand, and then to validate models primarily by comparing time series plots versus the observed experimental results. This paper reports our experiences in designing and building a modeling support environment (MSE) for cell cycle models. We describe improvements to the development process for cell cycle models by (a) identifying the key elements of the existing modeling process, (b) applying simulation methodology to construct a revised modeling process, and (c) building and testing software that supports the revised modeling process.