The FAIRDOMHub

11 items tagged with 'Clock'.

Neurospora Circadian Clock 3-variable model - PLM_51, version 1

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
...

Contributor: 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...

Created: 10th Jan 2019 at 17:41

Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, version 2

Millar group, PlaSMo model repository

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
...

Contributor: 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: No organisms

Models: Arabidopsis clock models P2011.1.2 and P2011.2...., Arabidopsis clock models P2011.1.2 and P2011.2....

SOPs: No SOPs

Data files: SBSI output from optimisation 26-30 July 2013, ..., Unpacked SBSI optimisation results, PLM_71_ 2

Created: 10th Jan 2019 at 17:39, Last updated: 24th Jan 2019 at 19:18

Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, version 1, SUBMITTED

PlaSMo model repository

Originally submitted model file for PLaSMo accession ID PLM_71, version 1

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Contributor: BioData SynthSys

Model type: Not specified

Model format: SBML

Environment: Not specified

Organism: Not specified

Investigations: Millar, Andrew (ex-PlaSMo models)

Studies: Arabidopsis clock models P2011.1.2 and P2011.2....

Modelling analyses: Arabidopsis clock models P2011.1.2 and P2011.2....

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Created: 10th Jan 2019 at 17:47, Last updated: 22nd Jan 2019 at 18:17

Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, version 2, SUBMITTED

TiMet, PlaSMo model repository

Originally submitted model file for PLaSMo accession ID PLM_71, version 2

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Contributor: 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 models P2011.1.2 and P2011.2....

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Created: 10th Jan 2019 at 17:47, Last updated: 24th Jan 2019 at 19:22

P2011.1.2_directupload

Millar group

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

Creator: Andrew Millar

Contributor: 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

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Created: 27th Mar 2018 at 17:16

Arabidopsis clock model P2011.1.2

Millar group

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

Contributor: 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... and 1 hidden item

Studies: 2 hidden items

Modelling analyses: 2 hidden items

Download

Created: 1st Feb 2017 at 22:32, Last updated: 27th Mar 2018 at 15:54

Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT

Regulation of flowering time in natural conditions

(Show All)

Abstract (Expand)

BioRxiv preprint:

Authors: Hannah A Kinmonth-Schultz, Melissa J MacEwen, Daniel Seaton, Andrew Millar, Takato Imaizumi, Soo-Hyung Kim

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/267104

Citation: Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT

Created: 2nd May 2019 at 15:34, Last updated: 2nd May 2019 at 15:37

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Millar group

Abstract (Expand)

bioRxiv preprint 2017 Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic ...

Authors: Daniel Seaton, Alexander Graf, Katja Baerenfaller, Mark Stitt, Andrew Millar, Wilhelm Gruissem

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/182071

Citation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Created: 16th Nov 2017 at 13:06, Last updated: 16th Nov 2017 at 13:11

Linking circadian time to growth rate quantitatively via carbon metabolism

Millar group

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Abstract (Expand)

Predicting a multicellular organism's phenotype quantitatively from its genotype is challenging, as genetic effects must propagate up time and length scales. Circadian clocks are intracellular ...

Authors: Yin Hoon Chew, Daniel Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Alison M. Smith, Mark Stitt, Andrew Millar

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/105437

Citation: Linking circadian time to growth rate quantitatively via carbon metabolism

Created: 4th Sep 2017 at 13:53, Last updated: 4th Sep 2017 at 13:58

Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf

Millar group

Abstract (Expand)

The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary ...

Authors: B. Wenden, D. L. Toner, S. K. Hodge, R. Grima, Andrew Millar

Date Published: 13th Apr 2012

Journal: Proc Natl Acad Sci U S A

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.

Created: 10th Mar 2017 at 17:19

Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature

Millar group

Abstract (Expand)

Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, ...

Authors: Daniel Seaton, R. W. Smith, Y. H. Song, D. R. MacGregor, K. Stewart, G. Steel, J. Foreman, S. Penfield, T. Imaizumi, Andrew Millar, K. J. Halliday

Date Published: 21st Jan 2015

Journal: Mol Syst Biol

PubMed ID: 25600997

Citation: Mol Syst Biol. 2015 Jan 19;11(1):776. doi: 10.15252/msb.20145766.

Created: 6th Feb 2017 at 13:54