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 (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].

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, rescales to match the absoulte RNA levels in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3. The model development is described in more detail in the 'Model Evolution' document attached.

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 and the final publication are linked here: the models and analysis are identical in both.

A Snapshot of this investigation is available here, at Zenodo, and at University of Edinburgh's DataShare resource.

Investigation position:

help Creators and Submitter
Millar, A., & Urquiza Garcia, U. (2021). Absolute units in Arabidopsis clock models up to U2020.3. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.INVESTIGATION.170.3
Note: This is a citation for Snapshot 3 of this Investigation, the contents of which may vary from what is shown on this page.
Snapshot 3 (4th Aug 2021) DOI
Snapshot 2 (31st Aug 2021) DOI
Snapshot 1 (31st Jul 2021) DOI Exported to Zenodo

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Created: 6th Dec 2017 at 22:38

Last updated: 9th Sep 2021 at 14:53

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