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. <strong>Original model</strong>: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, <a href="http://dx.doi.org/10.1038/msb.2012.6">http://dx.doi.org/10.1038/msb.2012.6</a>
- Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412
- Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
<strong>This model</strong> 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:
- updated formulation for light input (now uses ISSF of Adams et al. J Biol Rhythms 2012),
- 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.
- Parameter constraints added for SBSI optimisation.
- 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.
Flis et al. (2015). ...open infrastructure.... Royal Society Open Biology. Retrieved from: http://dx.doi.org/10.1098/rsob.150042
This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.
Originally submitted to PLaSMo on 2013-06-15 14:08:52
SEEK ID: https://fairdomhub.org/assays/820
Investigation: Millar, Andrew (ex-PlaSMo models)
Biological problem addressed: Gene Regulatory Network
Organisms: Arabidopsis thaliana
Created: 10th Jan 2019 at 17:39
Last updated: 20th Dec 2019 at 12:07