Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).
The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model: Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was available only to collaborators. It is included here for completeness.
Version 2 links to the same GitHub repository, where the MATLAB model files have been annotated by Dr. Daniel Seaton for the convenience of new users, and are now public. This version of the FMv2 model is released in June 2018 under the Apache 2.0 license, included with the files.
Model development will probably end in 2018, with an update that streamlines the simulation process.
2019: the Quantitative Plant resource now redirects here to give access to the FMv2 - https://quantitative-plant.org/model/ArabidopsisFrameworkModel
SEEK ID: https://fairdomhub.org/models/248?version=2
1 item is associated with this Model:Organism: Arabidopsis thaliana
Model type: Not specified
Model format: Matlab package
Execution or visualisation environment: Matlab
Model image: No image specified
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Created: 6th Feb 2017 at 16:43
Last updated: 20th Dec 2019 at 18:43

Version History
Version 2 (latest) Created 24th Jun 2018 at 22:55 by Daniel Seaton
FAIRDOMHub Version 2 of the FMv2 model has annotated MATLAB files, released from a GitHub repository that was made public in June 2018.
Related items
Projects: Millar group, TiMet
Institutions: University of Edinburgh

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

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
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Programme: SynthSys
Public web page: http://timing-metabolism.eu/
Organisms: Arabidopsis thaliana, Ostreococcus tauri
Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated in 2022, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU FP7 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. The updates are not changing the core data or the FMv2 model that has been ...
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
Snapshots: Snapshot 1
Modelling and experiments for FMv2 components.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Composition of FMv2, Simulating clock gene expression with model P2011.1.2, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Arabidopsis - starch and the circadian clock, M..., Chew_et_al_2014_Framework_Model version 1, Matl..., Framework Model v2, Modelling circadian regulation of flowering tim...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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: 6th Feb 2017
Publication Type: Tech report
DOI: 10.1101/105437
Citation: biorxiv;105437v1,[Preprint]
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar
Date Published: 6th Feb 2017
Publication Type: Tech report
DOI: 10.1101/105437
Citation: biorxiv;105437v2,[Preprint]