Studies

The P2011 model (linked in the Assay below) was rescaled to match TiMet RNA data in clock mutants from Flis et al. 2015, also linked here as separate mean and SD files. The raw TiMet data is available elsewhere on FAIRDOMHub.

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Originally submitted to PLaSMo on 2012-05-31 22:18:27

P2011 model from PLM_43 version 6, optimised by Andrew Millar with SBSI PGA optimisation. A limited parameter set were free to optimise over < 10-fold range (less for RNA degradation rates), against ROBuST RNA data for clock genes in WT and mutants at 17C in LD, and period data in the same mutants in LL. The full SBSI costing is included, using costs from mid-June 2012 (note that costs returned with original optimisation in May were incorrectly reported).Originally submitted to PLaSMo on ...

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 ...

Creator - Dr. Daniel D. Seaton. Graphical overview of Arabidopsis clock model P2011 in SBGN, from SBGN-ED in VANTED v2. N.B. to pass PlaSMo validation before update, the tag was back-edited from the correct string to in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached. Related PublicationsFlis et al. (2015). Open ...

Model of the arabidopsis circadian clock obtained from the Bio-PEPA model. The model is based on Alexandra Pokhilko's 2010 deterministic model and includes a scaling factor omega to translate from continuous "concentrations" to discrete amounts. Light function is a smooth function switching between 0 and 1, and is parameterised in order to allow to automate experimentation with different light conditions and photoperiods.Related PublicationsMaria Luisa Guerriero, Alexandra Pokhilko, Aurora Piñas ...

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.

Originally submitted to PLaSMo on 2011-07-16 12:31:04