Minnesota/11 June 2009

Most group members continued to learn MATLAB, Linux commands, and html as issues presented themselves. One major setback was the realization that designgui could not produce non-linear parameter variation. This is unfortunate for the following reason:

Essentially, the aTc concentrations in the models without a lac operon vary from 0 to 260 molecules per cell, but not linearly. The concentrations tested are 0, 1, 13, 65, 130, 260 molecules per cell. Without the ability to vary this parameter non-linearly we are forced to created 6 separate .nc-files for each model we run through the supercomputer. A work around will try to be determined, or the designGUI modified in order to facilitate this in the coming weeks. This is important to get done before ever attempting a TTL model since with a lac operon, IPTG becomes a factor, and without non-linear variation of parameters 36 separate .nc-files would need to be created per model to get accurate results.