This morning there were a series of presentations about the 
Biology Workbench. I've done the Biology Workbench to death, so I hung out during the presentations, but was playing with netlogo instead. One of the participants had the idea of creating a model of gene expression, so I built a prototype this morning. It was great fun and gave me a chance to try out some things I hadn't done before. The first version had the products of transcription acting as transcription factors. Once I realized that, I added some ribosomes that would transform the RNAs into proteins. Now that we have a working system, the next step is to do an analysis of the problem space and see what versions we might want to build to allow students to discover particular principles about these systems. I'll probably post these eventually so that everyone can play with them.
Here's the model, if anyone wants to play with it.