This model is derived from Biomodels 299 - the Leloup et al Neurospora clock model. This variant contains an embedded light-forcing function (SBO:000475) that provides a periodic light input. In this model, after 72h of LD12:12, the amplitude of Vs ( the light dependent parameter ) increases to 4.1, leading to chaotic oscillations. For this to happen, the periodic light function needs to produce a square-wave pattern. Execution of this model will result in the behaviour depicted in Figure 2D
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Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Adams, Richard
Study: Neurospora Circadian Clock 3-variable model - P...
Organisms: No organisms
Models: Neurospora Circadian Clock 3-variable model - P..., Neurospora Circadian Clock 3-variable model - P...
SOPs: No SOPs
Data files: A SED-ML archive file containing the model and ..., After 72 hrs, the light function increases to 4..., Instructions on how to use the SED-ML archive, ..., SEDX Archive reproducing a phase response param...
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.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
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
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Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis clock models P2011.1.2 and P2011.2....
Organisms: Arabidopsis thaliana
Models: Arabidopsis clock model P2011.2.1 - PLM_71, ver..., Arabidopsis clock model P2011.2.1 - PLM_71, ver...
SOPs: No SOPs
Data files: SBSI output from optimisation 26-30 July 2013, ..., Unpacked SBSI optimisation results, PLM_71_ 2
Originally submitted model file for PLaSMo accession ID PLM_71, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.1.2 - PLM_71, ver...
Originally submitted model file for PLaSMo accession ID PLM_71, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.2.1 - PLM_71, ver...
Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.
Creator: Andrew Millar
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in Arabid...
Studies: 1 hidden item
Modelling analyses: 1 hidden item
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.
http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1
Creator: Andrew Millar
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t..., Prediction and analysis of phenotypes in Arabid...
Studies: Rescaling the P2011 model to match RNA data and 1 hidden item
Modelling analyses: 2 hidden items
Abstract
Authors: Karl Fogelmark, Carl Troein
Date Published: 17th Jul 2014
Publication Type: Not specified
DOI: 10.1371/journal.pcbi.1003705
Citation: PLoS Comput Biol 10(7) : e1003705
Abstract
Authors: Hannah A Kinmonth-Schultz, Melissa J MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/267104
Citation: Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
Abstract (Expand)
Authors: Daniel Seaton, Alexander Graf, Katja Baerenfaller, Mark Stitt, Andrew Millar, Wilhelm Gruissem
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/182071
Citation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Alison M. Smith, Mark Stitt, Andrew J Millar
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/105437
Citation: Linking circadian time to growth rate quantitatively via carbon metabolism
Abstract (Expand)
Authors: B. Wenden, D. L. Toner, S. K. Hodge, R. Grima, A. J. Millar
Date Published: 13th Apr 2012
Publication Type: Not specified
PubMed ID: 22496591
Citation: Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6757-62. doi: 10.1073/pnas.1118814109. Epub 2012 Apr 10.
Abstract (Expand)
Authors: D. D. Seaton, R. W. Smith, Y. H. Song, D. R. MacGregor, K. Stewart, G. Steel, J. Foreman, S. Penfield, T. Imaizumi, A. J. Millar, K. J. Halliday
Date Published: 21st Jan 2015
Publication Type: Not specified
PubMed ID: 25600997
Citation: Mol Syst Biol. 2015 Jan 19;11(1):776. doi: 10.15252/msb.20145766.