U2020.1

Model derived from P2011.1.2 in which the steady state assumptions for the Evening complex in P2011 were eliminated. After eliminating
these assumptions the model was fitted to the original dynamics of P2011.1.2 for the networks WT, lhycca1, prr79, toc1, gi, ztl.
In particular for the lhycca1 double mutant only the repressive "arms" (edges) for cL were set to zero.
The parameter values or cP and for COP1 variables were fixed as these have been fitted before in Pokhilko et al 2012 Mol Sys Bio.

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U2020.2

Model derived from U2020.1 in which the transcription rates were rescaled to match the scale of TiMet data set.
The gmX parameters in the model were fitted numerically. This has equivalent dynamics to P2011.1.2.

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U2020.3

U2020.2 derived model in which the was fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters.
The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl.
The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the
product of scaling factor and either transcription or translation, the latter required for painting the dynamic in the system.


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U2020.4

Model derived from U2020.1 for which the way the PRRs are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression.
This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression.
F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression pattern.
This was covered by F2016 were a formal study on the type or regulation results in sharper RNA expression profile for the PRRs.

Variables for the new regulation were proposed, which did not feedback into the model. This was done to obtain a correct shape for the new regulation.
Perfect data from U2020.1 was generated for the networks in the TiMet data set including also ztl mutant. This was the case for both transcript and protein profiles.
The next step was to substitute the old PRR regulation for the new regulatory wiring using the parameters obtained from the mentioned fitting.
Then new architecture was fitted to U2020.1 resulting in equivalent dynamics for the TiMet variables and networks including ztl.
In all these fittings the parameters for cP and COP1 were fixed as they have been fitted before in Pokhilko et al 2012 Mol Sys Bio

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U2020.5


Model derived from U2020.4 by fitting the scaling factors for matching TiMet data set and mutant networks.

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U2020.5 derived model in which the was fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters.
The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl.
The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the
product of scaling factor and either transcription or translation, the latter required for painting the dynamic in the system.
