Arabidopsis clock model P2011.1.2 - PLM_71, version 1

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=""></a>
<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:
  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). infrastructure.... Royal Society Open Biology. Retrieved from:

Version Comments

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

help Creators and Submitter

Views: 1465

Created: 10th Jan 2019 at 17:39

Last updated: 20th Dec 2019 at 12:07

help Tags

This item has not yet been tagged.

Related items

Powered by
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies