Arabidopsis clock model P2011.1.2
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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

SEEK ID: https://fairdomhub.org/models/243?version=1

1 item is associated with this Model:

PLM_71.xml (XML document - 87.2 KB)

Organism: Arabidopsis thaliana

Model type: Ordinary differential equations (ODE)

Model format: SBML

Execution or visualisation environment: JWS Online

Model image: No image specified

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Creators and Submitter

Creator

Andrew Millar

Submitter

Andrew Millar

License

Creative Commons Attribution 4.0 International

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Views: 3696 Downloads: 155 Runs: 0

Created: 1st Feb 2017 at 21:32

Last updated: 27th Mar 2018 at 13:54

Version History

Version 1 (earliest) Created 1st Feb 2017 at 21:32 by Andrew Millar

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

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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

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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

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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

Absolute units in Arabidopsis clock models up to U2020.3

Millar group

All creators

Andrew Millar

Uriel Urquiza Garcia

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.

Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...

Submitter: Andrew Millar

Studies: P2011, U2019 and U2020 models and modelling resources, Rescaling the P2011 model to match RNA data

Assays: P2011.1.2, Reproducibility tool set, TiMet RNA timeseries data and starting models, U2019/U2020 models

Snapshots: Snapshot 1, Snapshot 2, Snapshot 3

DOI: 10.15490/fairdomhub.1.investigation.170.3

Created: 6th Dec 2017 at 21:38, Last updated: 9th Sep 2021 at 12:53

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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

Rescaling the P2011 model to match RNA data

Millar group

All creators

Andrew Millar

Uriel Urquiza Garcia

The P2011 model (linked in the Assay below) was rescaled to match TiMet RNA data in clock mutants from Flis et al. 2015, also linked here as separate mean and SD files. The raw TiMet data is available elsewhere on FAIRDOMHub.

Submitter: Andrew Millar

Investigation: Absolute units in Arabidopsis clock models up t...

Assays: TiMet RNA timeseries data and starting models

Snapshots: No snapshots

Created: 6th Dec 2017 at 21:46, Last updated: 29th Jul 2021 at 19:33

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Simulating clock gene expression with model P2011.1.2

Millar group, TiMet

All creators

Andrew Millar

Comparison of simulated wild-type and prr7prr9 double mutant under 12L:12D cycles. Simulation with CVODE simulator via SBSI v1.5 framework.

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), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm)

Models: Arabidopsis clock model P2011.1.2, P2011.1.2_directupload

SOPs: No SOPs

Data files: P2011.1.2 simulations and data in prr7 prr9 mut..., P2011.1.2 simulations of clock genes under LD c..., P2011.1.2 simulations vs. data for WT, normalis..., TiMet WP1.1 qRT-PCR LD to LL and DD

Snapshots: No snapshots

Created: 1st Feb 2017 at 21:29, Last updated: 15th Apr 2022 at 10:35

TiMet RNA timeseries data and starting models

Millar group

All creators

Andrew Millar

Uriel Urquiza Garcia

RNA timeseries data for Arabidopsis Col wild-type plants and clock mutants, as separate mean and SD files. The raw data is available on BioDare.ed.ac.uk, and is linked as 'Attribution' from elsewhere on FAIRDOMHub.

The starting models are included here in their original forms, the P2011 model as an SBML L3V1 model file, and the KF2014 model of Fogelmark et al. shared as SBML; both prepared by Uriel Urquiza.

Submitter: Andrew Millar

Biological problem addressed: Gene Regulatory Network

Investigation: Absolute units in Arabidopsis clock models up t...

Study: Rescaling the P2011 model to match RNA data

Organisms: No organisms

Models: Arabidopsis clock model P2011.1.2, F2014 all parameters in SBML, F2014.1 - PLM_1030, version 1, SUBMITTED, F2014.1.2 with stepfunction and 1 hidden item

SOPs: No SOPs

Data files: Processed TiMet WP1.1a RNA data, SD, Processed TiMet WP1.1a RNA data, mean

Snapshots: No snapshots

Created: 6th Dec 2017 at 21:48, Last updated: 2nd Aug 2021 at 21:48

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Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Millar group

All creators

Andrew Millar

Abstract (Expand)

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA … profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.

Authors: A. Flis, A. P. Fernandez, T. Zielinski, V. Mengin, R. Sulpice, K. Stratford, A. Hume, A. Pokhilko, M. M. Southern, D. D. Seaton, H. G. McWatters, M. Stitt, K. J. Halliday, A. J. Millar

Date Published: 16th Oct 2015

Publication Type: Not specified

PubMed ID: 26468131

Citation: Open Biol. 2015 Oct;5(10). pii: 150042. doi: 10.1098/rsob.150042.

Created: 1st Feb 2017 at 21:00, Last updated: 8th Dec 2022 at 17:26

Arabidopsis clock model P2011.1.2 Version 1

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Submitter

Version History

Version 1 (earliest) Created 1st Feb 2017 at 21:32 by Andrew Millar

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Arabidopsis clock model P2011.1.2
Version 1