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

The models in this record were published in Flis et al. Royal Society Open Biology 2015. Their original IDs in the PlaSMo resource and IDs in Biomodels are given below. Please select files for download from the 'Related Items' list or the object tree/graph, below. 'SUBMITTED' is the original model version; 'SIMPLIFIED' removes SBML elements that were incompatible with SloppyCell software.

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; Biomodels ID BIOMD0000000597, https://www.ebi.ac.uk/biomodels/BIOMD0000000597. The model's dynamics are 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. Biomodels ID BIOMD0000000598, https://www.ebi.ac.uk/biomodels/BIOMD0000000598.

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

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

SEEK ID: https://fairdomhub.org/studies/488

Millar, Andrew (ex-PlaSMo models)

Projects: Millar group, PlaSMo model repository

BioData SynthSys

Experimentalists: Not specified

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Andrew Millar
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Created: 10th Jan 2019 at 17:38

Last updated: 24th Jan 2019 at 19:14

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