Chew_et_al_2014_Framework_Model version 1, Matlab and Simile Version 1
This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.
The FMv1 links the following sub-models:
- Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model
- Part of the Christophe et al 2008 Functional-Structural Plant Model
- Chew et al 2012 Photothermal Model
- Salazar et al 2009 Photoperiodism Model
To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php and follow the instructions detailed in the PlaSMo record linked from this Model.
SEEK ID: https://fairdomhub.org/models/247?version=1
3 items (and an image) are associated with this Model:-
134MATLAB%20Framework%20Model.zip (Zip file - 28.8 KB)
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1020Framework%20Model%20in%20Simile.zip (Zip file - 1010 KB)
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http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_76 (Website)
Organism: Arabidopsis thaliana
Model type: Not specified
Model format: Matlab package
Execution or visualisation environment: Matlab
Model image: (Click on the image to zoom) (Original)
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Creators and Submitter
Views: 2085 Downloads: 135
Created: 6th Feb 2017 at 14:08
Last updated: 22nd Aug 2018 at 13:40
Last used: 23rd May 2022 at 11:12
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Version History
Version 1 Created 6th Feb 2017 at 14:08 by Andrew Millar
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Related items
Projects: Millar group, TiMet
Institutions: University of Edinburgh
https://orcid.org/0000-0002-9258-583X
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh
https://orcid.org/0000-0003-1756-3654
SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated 2022 as bioRxiv https://doi.org/10.1101/105437v2, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU TiMet project, https://fairdomhub.org/projects/92.
This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. NB ...
Submitter: Andrew Millar
Studies: Analysis of Framework Model version 2 (FMv2), Construction of Framework Model version 2 (FMv2), Test of FMv2, follow-on: mechanisms of malate/fumarate accumulation, Test of FMv2, photoperiodic flowering and hypocotyl elongation, Test of FMv2, study Gibberellins 1, Test of FMv2, study Laurel & Hardy 1, Test of FMv2, study Laurel & Hardy 2, Test of FMv2, study Laurel & Hardy 3, Tests of FMv2, compilations and figures
Assays: Assimilation and partitioning of 14CO2 at night, Biomass and metabolites, Biomass and metabolites, Biomass and metabolites, Biomass, leaf area and gas exchange data, Biomass, leaf number and metabolites, Circadian period analysis, Composition of FMv2, FMv2 simulation, FMv2 simulation, FMv2 simulation, Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants, Relationship among FMv2 outputs, Sensitivity analysis of FMv2, Simulating clock gene expression with model P2011.1.2, Thiamine vitamers, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).
Submitter: Andrew Millar
Studies: Construction of Framework Model v1, Test of FMv1, growth study of Col-0 accession in 12L:12D, Test of FMv1, growth study of Col-0 accession in 5 photoperiods, Test of FMv1, growth study of other accessions and transgenic line in 12...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version, Gas exchange of Fei-0 and Ler plants in 12hL:12hD, Growth of Col-0 and 35S:miR156 plants in 12hL:12hD, Growth of Col-0 in 12hL:12hD, Growth of Col-0 plants in 5 photoperiods, Growth of Fei-0 and Ler plants in 12hL:12hD
Modelling and experiments for FMv2 components.
The FMv1 was constructed from 4 existing models, with Matlab and Simile versions.
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version
Combination of multiple sub-models to form Framework Model version 2
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
In future we should split these versions into separate Assays, and link to the four, original component models, when they are imported with the PlaSMo resource into FairdomHub (expected late 2018)
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Arabidopsis Framework Model v1, predicting rose...
Abstract (Expand)
Authors: Y. H. Chew, B. Wenden, A. Flis, V. Mengin, J. Taylor, C. L. Davey, C. Tindal, H. Thomas, H. J. Ougham, P. de Reffye, M. Stitt, M. Williams, R. Muetzelfeldt, K. J. Halliday, A. J. Millar
Date Published: 10th Sep 2014
Publication Type: Not specified
