Framework Model v2
Version 2

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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:

https://github.com/danielseaton/frameworkmodel (Website)

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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Creators and Submitter

Creators

Daniel Seaton
Yin Hoon Chew
Andrew Millar

Submitter

Daniel Seaton

License

Other (Open)

Activity

Views: 4028

Created: 6th Feb 2017 at 15:43

Last updated: 20th Dec 2019 at 17:43

Version History

Version 2 (latest) Created 24th Jun 2018 at 20:55 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.

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People (3)
Programmes (1)
Projects (2)
Investigations (1)
Studies (1)
Assays (1)
Publications (2)

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Yin Hoon Chew

Projects: Millar group, TiMet

Institutions: University of Edinburgh

https://orcid.org/0000-0002-9258-583X

Andrew Millar

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

Expertise: circadian rhythms, arabidopsis thaliana, Mathematical modelling, Data Management, Molecular Biology, Genetics, Deterministic modelling of gene regulation networks, Systems Biology

Tools: Transcriptomics, Proteomics, Deterministic models, Stochastic models, SBML

Daniel Seaton

Projects: Millar group, TiMet, Regulation of flowering time in natural conditions

Institutions: University of Edinburgh

https://orcid.org/0000-0002-5222-3893

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SynthSys

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

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Millar group

Andrew Millar's research group, University of Edinburgh

Programme: SynthSys

Public web page: http://www.amillar.org

Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri

TiMet

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

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Prediction and analysis of phenotypes in the Arabidopsis clock mutant <i>prr7 prr9</i> using the Framework Model v2 (FMv2)

Millar group, TiMet

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All creators

Andrew Millar

Yin Hoon Chew

Daniel Seaton

Virginie Mengin

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

DOI: 10.15490/fairdomhub.1.investigation.123.1

Created: 1st Feb 2017 at 20:21, Last updated: 3rd Nov 2022 at 13:19

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Construction of Framework Model version 2 (FMv2)

Millar group, TiMet

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Andrew Millar

Yin Hoon Chew

Daniel Seaton

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

Created: 1st Feb 2017 at 20:25, Last updated: 15th Apr 2022 at 10:35

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Composition of FMv2

Millar group, TiMet

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All creators

Andrew Millar

Yin Hoon Chew

Daniel Seaton

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...

Study: Construction of Framework Model version 2 (FMv2)

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

Created: 1st Feb 2017 at 21:26, Last updated: 15th Apr 2022 at 10:35

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Linking circadian time to growth rate quantitatively via carbon metabolism

Millar group

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Yin Hoon Chew

Daniel Seaton

Andrew Millar

Abstract (Expand)

Summary paragraph 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 …length scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour, from sleep/wake cycles in mammals to flowering in plants 1–3 . Clock genes are rarely essential but appropriate alleles can confer a competitive advantage 4,5 and have been repeatedly selected during crop domestication 3,6 . Here we quantitatively explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for growth of Arabidopsis thaliana 7–9 . The model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants. Altered night-time metabolism of stored starch accounted for most but not all of the decrease in whole-plant growth rate. Altered mobilisation of a secondary store of organic acids explained the remaining defect. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.

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]

Created: 4th Sep 2017 at 11:53, Last updated: 8th Dec 2022 at 17:26

The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

TiMet

(Show All)

All authors

Yin Hoon Chew

Daniel Seaton

Virginie Mengin

Andrew Millar

Abstract (Expand)

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that … control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits. This work updates the first biorXiv version, February 2017,with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.

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

Framework Model v2 Version 2

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Submitter

Version History

Version 2 (latest) Created 24th Jun 2018 at 20:55 by Daniel Seaton

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Framework Model v2
Version 2