Absolute units in Arabidopsis clock models up to U2020.3

Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2 (first version was U2017.2), then reoptimises globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model. [The first version U2017.3 also matched the protein levels that were independently predicted by a simple translation model, from those RNA levels]. 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 (first version U2017.2) model, to create the U2020.1 (first version U2018.1) 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 (first U2018.2) model, and performs a global reoptimisation as above to form U2020.3 (U2018.3). Early versions of these models with internal nomenclature remain private and are not included in the static Snapshot shared with the publication. 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 here. The DOI for the publication was not yet available.