This folder contains the scripts necessary to reproduce the computational results of "Convergence in Parameters and Predictions using Computational Experimental Design" by David R Hagen, Jacob K White, and Bruce Tidor published in Interface Focus in 2013. Please direct any questions to the corresponding author.

The results were generated using Matlab 2008b. There are three main types of files:

(1) ".m" files are mostly scripts that generate the data and plot the figures. In every case, a computer cluster is required to parallelize certain portions of the code, which are clearly marked in the scipts.

(2) ".mat" files are shatshots of Matlab workspaces after the scripts were run so that you can look at the data without having to generate it yourself.

(3) ".fig" files are the Matlab figures that are in the paper.

The main results of that paper, as opposed to the supplementary results, are prefixed with "Main" for easy browsing.

There is a copy of KroneckerBio, the biological modeling toolbox developed in the Tidor lab by David Hagen, Joshua Apgar, Jared Toettcher, Jacob White, and Bruce Tidor. This is the version used to generate the results of this paper; if you would like to use KroneckerBio for your own work, you are encouraged to get the latest version from the corresponding author. All code is released under the MIT license, except for a few files taken from other sources with their respective licenses. All data and figures are CC-BY.