Starting from the P2011 model of the circadian clock in Arabidopsis thaliana, this project corrects theoretical issues (steady-state binding assumption for the Evening Complex, EC) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises model parameters globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model.
This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.2 model, to create the U2020.1 model, then also rescales to match the protein levels that were independently predicted by a simple translation model from those RNA levels, in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3.
The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files and documentation are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked here. The DOI for the publication was not yet available.
The work was funded by a PhD scholarship from Conacyt, Mexico to U. Urquiza Garcia.
Urquiza Garcia, Uriel; Millar, Andrew J. (2021). Absolute units in Arabidopsis clock models up to U2020.3, 2016-2020 [dataset]. SynthSys. School of Biological Sciences. University of Edinburgh. https://doi.org/10.7488/ds/3109.