Absolute units in Arabidopsis clock models up to U2020.3

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021. Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) 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 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 U2019.1 model, to create the U2020.1 model, then also rescales to match the 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 are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked inside the archive structure. The DOI for the publication was not yet available but is now: 10.1093/insilicoplants/diab022. This version 3 replaces 10.5281/zenodo.5150823 (version 2), as model files for the earlier KF2014 models were omitted in error from versions 1 and 2. There are no other changes.

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.