U2020_5 - Urquiza 2025 Arabidopsis circadian clock

SBML L3V1 format model U2020.5 of the clock gene circuit in the plant Arabidopsis thaliana, inspired by the P2011 model, published in Pokhilko et al Mol Syst Biol 2012 (Biomodels BD000..0412). The U2019 version uses very similar interactions to P2011, where the combined LHY/CCA1 component indirectly activates the wave of PRR gene expression, whereas the U2020 version uses both indirect activation and inter-PRR repression. This .5 version has parameters scaled to yield absolute units for both RNAs and proteins (copy number per cell), whereas the .3 versions of each model are scaled to match only the absolute RNA level data (MODEL2212200002 is U2020.3, for example). SBML files were verified using COPASI software. The full process is described in Urquiza Garcia et al. Molecular Systems Biology, 2025.