This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached to version 1 of this model (the published SBML is correct). The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including:
- the Evening Complex genes (ELF4, ELF3, LUX),
- light-regulated degradation of ELF3 by COP1,
- TOC1 as a repressor rather than an activator of LHY/CCA1.
Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.. Mol. Syst. Biol. 8: 574.. Retrieved from: http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html
Version 2 of the model includes the StepFunction. Note that we have not yet removed the original light function parameter names, they are now non-functional.
2012-06-01 17:29:46 3 amillar2 firstname.lastname@example.org
The SBML for this version uses the lightfunction (as in Mol Syst Biol 2012 paper) to represent the light-dark cycle. It is assigned to parameter name L, which is used in the model reactions.
However, the internal parameters of lightfunction have default Copasi ID's, parameter_1 to parameter_6, with names that match the publication (photperiod, etc.). A COPASI file for this model is also attached.
This model is equivalent to the published version, referred to as P2011.1.1 in our later paper (Flis et al. RSOB 2015).
Originally submitted to PLaSMo on 2012-03-07 12:15:12
SEEK ID: https://fairdomhub.org/assays/840
Investigation: Millar, Andrew (ex-PlaSMo models)
Biological problem addressed: Gene Regulatory Network
Organisms: Arabidopsis thaliana
Created: 10th Jan 2019 at 17:40
Last updated: 25th Jun 2019 at 13:38