Clocksim

Accompanying files for

Karl Fogelmark and Carl Troein
Rethinking transcriptional activation in the Arabidopsis circadian clock
PLoS Computational Biology 10, e1003705 (2014)
DOI 10.1371/journal.pcbi.1003705

• clocksim.tar.gz contains the C++ source code for clocksim, which is is a program for fitting and evaluating ODE models, in particular for clocks. Compile the program using GNU Make, and read the README file for instructions on how to use it.
• data.tar.gz contains the 800+ time courses compiled from the literature. The files are named in a fairly systematic way according to their contents (light conditions, reporter, mutant etc.). Comments in the files describe the contents briefly, and the original paper is cited (usually with a link).
• F2011.tar.gz contains the F2014 model of the Arabidopsis circadian clock, in the format expected by clocksim. The equations include the full set of alterations needed to simulate the many mutants. The eight best parameter sets are included. The data directory should be placed (or linked to) in the F2014 directory to allow clocksim to find the files.
• P2011.tar.gz and P2012.tar.gz contain the P2011-P2012 models of the clock. As with F2014, they require the data directory to be linked or copied into their respective directories.