I recently discovered an interesting piece of open-source software, the CESE single-cell simulator. It’s based on Java and runs on a number of platforms.
The point of this simulator is strictly to run single-cell electrophysiological models. It comes with a few of the staples in the field (like the Luo-Rudy dynamic model), and you can buy more recent/complex models from a company called Simulogic. Alternatively, there are directions on the site for designing your own models.
Unfortunately, the program currently displays the output of all of the selected variables on the same plot, rather than breaking the plot into several panels, one for each current. The latter is the way we typically look at model data. Furthermore, I don’t see a way to import experimental data traces for comparison. I also had some rendering issues with pull-down selectors in Mac OS X’s Java implementation.
We currently have our own single-cell simulator with an ugly but functional GUI, linked to the ionic models in our tissue simulator. However, it might be nice going forward to make our models compatible with CESE, and to work with the CESE developers to improve the view mode. It would be nice to have CESE as a standard platform for model development.
If you want to download it and try it out, you just need a working Java installation, and you can get CESE itself here. Check the built-in help for a tutorial.
Have you used CESE before? What did you think? If you download it and try it out, please post something about your experience here as well (or email me).