U2019/U2020 models

Collection of clock models that rescale transcript variables to account for absolute units. The relationship between models is summarised in the attached 'model evolution' document and in more detail in the linked publications (preprint version linked in the Snapshot; publication Urquiza and Millar, In Silico Plants 2021 did not have a DOI when Snapshot was created).

Each model is presented three times,

    • without a light:dark cycle,
    • with an ISSF (Adams et al. JBR 2012) that is set up for LD 12h:12h cycles, and
    • with an ISSF that runs 10 LD cycles followed by an SBML Event that switches to constant light, matching published simulations.
  • in addition, U2019.3 and U2020.3 are presented as PDF documents listing the model as automatically-generated equations.

The "Model Evolution" document briefly describes the development of the models and relationships between them. The "Parameter Values" document lists all the parameter values of each model, and is identical to Supplementary Table 2 of the publication.

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Created: 7th May 2020 at 16:12

Last updated: 29th Jul 2021 at 20:04

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