A few weeks ago Randy and I talked about creating some Netlogo models of metabolism, to help students understand how the electron transport chain responds to various conditions: what happens when you poison ATP synthase or add uncouplers to the system. (Uncouplers allow protons to leak back into the mitochondrial matrix and make it hard to build a large enough proton motive force to manufacture ATP). A bunch of students missed the questions on the exam that dealt with uncouplers. I was thinking it would be a useful model to build as a stepping stone to building models on signal transduction, that could be an extension of the gene expression models I've already build. so build an 
Electron Transport model. It still needs some polishing, but it's pretty good already. I also built a php file that make it simpler to publish netlogo models -- you can just publish the .nlogo and .html files and the php file will parse the html file, stripping off the garbage and letting someone choose whether to invoke the model using netlogo 1.3 or netlogo 2.0.1. It means that I don't have to hand-edit anything if I want to update a model with revisions. While I was thinking about it, I grabbed a screenshot and made a picture for the GBI. Our previous chair stopped by to ask me a technical question and while we were waiting for his machine to reboot, I showed him the models I was working on. He was interested and said he thought I ought to patent them. I don't think it would be feasible to commercialize them, but I'm hoping we might be able to get a grant to support continued development.