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

Theoretical molecular biologists attempt to describe cellular processes and regulatory networks with continuous and discrete mathematical models. Previous practice has been to develop models largely by hand and then to validate them primarily by comparing time-series plots versus the observed experimental results. The authors report their experiences in designing and building a modeling support environment for cell cycle models. They describe improvements to the development process for molecular network models by (a) identifying the key elements of the existing modeling process, (b) incorporating simulation methodology into a revised modeling process, and (c) building and testing software that supports the revised modeling process.