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.
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.
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Absolute units in Arabidopsis clock models up t...
Study: 1 hidden item
Models: U2019.1, U2019.1_ISSF, U2019.1_ISSF_10xLD_LL, U2019.2, U2019.2_ISSF, U2019.2_ISSF_10xLD_LL, U2019.3, U2019.3_ISSF, U2019.3_ISSF_10xLD_LL, U2020.1, U2020.1_ISSF, U2020.1_ISSF_10xLD_LL, U2020.2, U2020.2_ISSF, U2020.2_ISSF_10xLD_LL, U2020.3, U2020.3_ISSF, U2020.3_ISSF_10xLD_LL
SOPs: No SOPs
Data files: No Data files
Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
Investigations: Absolute units in Arabidopsis clock models up t...
Assays: 1 hidden item
Date Published: 20th Mar 2021
Publication Type: Tech report
Date Published: 2019
Publication Type: Journal
Citation: in silico Plants 1(1),diz006
Authors: Karl Fogelmark, Carl Troein
Date Published: 17th Jul 2014
Publication Type: Not specified
Citation: PLoS Comput Biol 10(7) : e1003705