Studies

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 P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including: TOC1 as a ...

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 ...

This model is one of five new parameter sets for P2011, 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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...

This model is one of five new parameter sets for P2011, 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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.5.1 is public model ID PLM_1043, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...

This model is one of five new parameter sets for P2011, 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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.4.1 is public model ID PLM_1042, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...

This model is one of five new parameter sets for P2011, 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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...

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 ...

Altering the light:dark cycle of standard growth conditions and standard 'wild-type' Arabidopsis accession, with sucrose, starch and biomass data for whole rosettes

Standard growth conditions and standard 'wild-type' Arabidopsis accession, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data

Standard growth conditions and 'wild-type' Arabidopsis accessions other than Col-0 and the 35S:miR156 transgenics, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data

The FMv1 was constructed from 4 existing models, with Matlab and Simile versions.

Literature data used in the Seaton et al. 2017 study; data processing by Daniel Seaton.

Experimental data reported in the Seaton et al. 2017 study; data processing by Alex Graf. Part of the EU FP7 TiMet project.

Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.

Data analysis and modelling scripts and results for the Seaton et al. 2017 study, from Daniel Seaton.