Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, version 2

The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

This model file has two versions, P2011.1.2 and P2011.2.1.

P2011.1.2 is public model ID PLM_71 version 1. Dynamics identical to P2011.1.1 but changes:



  1. updated formulation for light input (now uses ISSF of Adams et al. J Biol Rhythms 2012),


  2. formula for parameters m1 and m2 revised in Copasi, to cL_m degradation to ensure light rate > dark rate. Value of m1 previously 0.54, now 0.3. Simulation in Copasi was identical to earlier version.


  3. Parameter constraints added for SBSI optimisation.


  4. ISSF set to match TiMet RNA data under LD-LL, including LDLL transition event at 314h.

P2011.2.1 is public model ID PLM_71 version 2, with parameters optimised by Andrew Millar using SBSI on server sbsidev1, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version.


Related Publications
Flis et al. (2015). ...open infrastructure.... Royal Society Open Biology. Retrieved from: http://dx.doi.org/10.1098/rsob.150042

Version Comments


This version is P2011.2.1, model ID PLM_71 version 2, with parameters optimised by Andrew Millar using SBSI on server sbsidev1 using SBSI as described in Flis et al. RSOB 2015.



The full optimisation run information from the SBSI software is attached as two .ZIP files. The run started 26 July 2013 and ended 30 July after 599 generations of the genetic algorithm. Results were downloaded from the server on 31 July but the unpacking process crashed and was completed 1 Aug 2013, hence the uniform dates in the second .ZIP.




Originally submitted to PLaSMo on 2013-06-15 14:08:52

SEEK ID: https://fairdomhub.org/assays/821

Modelling Analysis

BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

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Andrew Millar
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Created: 10th Jan 2019 at 17:39

Last updated: 24th Jan 2019 at 19:18

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