Current Software

We haven't completed and released any software yet. When we have, either the software itself or links to it will be here.

Previous Software

MCell

During his postdoctoral research, Rex was involved in the continuing development of the MCell stochastic reaction-diffusion simulation system.

MCell is developed and maintained by the Sejnowski Lab at the Salk Institute and the Stiles Lab at Pittsburgh Supercomputer Center and Carnegie Mellon University.

For current information, see the MCell pages on the West Coast or East Coast.

Jmalyze

Jmalyze is a program to analyze fluorescent ratiometric data (or single-channel intensity data) for calcium imaging in C. elegans; it was written by Rex during his graduate work and has not been updated since. C. elegans researchers who want a copy of Jmalyze should email Rex. Please note that the software comes with no support or documentation whatsoever; if you don't already know how to use it, please find a lab that is currently using it for training. Also, Jmalyze only reads MetaVue/Morph/Fluor .stk files or sets of single .tiffs. At some point there will be a new, lightly supported version once we start doing extensive calcium imaging experiments.