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.
SEEK ID: https://fairdomhub.org/studies/317
Absolute units in Arabidopsis clock models up to U2020.3
Projects: Millar group
Study position:
Experimentalists: Uriel Urquiza
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Created: 6th Dec 2017 at 21:46
Last updated: 29th Jul 2021 at 19:33
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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/0000-0003-1756-3654Projects: Millar group, PlaSMo model repository, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development, Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Institutions: University of Edinburgh, Heinrich Heine University of Düsseldorf
https://orcid.org/0000-0002-7975-5013SynthSys 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
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 ...
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...
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
SD values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
The ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Investigations: Absolute units in Arabidopsis clock models up t... and 1 hidden item
Studies: Rescaling the P2011 model to match RNA data and 1 hidden item
Assays: TiMet RNA timeseries data and starting models and 1 hidden item
Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
The ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Investigations: Absolute units in Arabidopsis clock models up t... and 1 hidden item
Studies: Rescaling the P2011 model to match RNA data and 1 hidden item
Assays: TiMet RNA timeseries data and starting models and 1 hidden item
Originally submitted model file for PLaSMo accession ID PLM_1030, version 1
Creators: BioData SynthSys, Uriel Urquiza Garcia, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
From published files, Uriel Urquiza created SBML models with all 8 parameter sets published, and versions of F2014.1 to simulate multiple clock mutants, using SloppyCell
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
F2014.1.1 becomes the published version, with SBML file originally created from SloppyCell by Uriel Urquiza - see separate file. then Andrew Millar converted into SBML L2V4 in Copasi and added ISSF for light input, using SBSI Stepfunction editor (see Adams et al. 2011 J Biol Rhythms).
Creators: Andrew Millar, Karl Fogelmark, Carl Troein
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
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
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t..., Prediction and analysis of phenotypes in the Ar...
Studies: Construction of Framework Model version 2 (FMv2), Rescaling the P2011 model to match RNA data
Assays: Simulating clock gene expression with model P20..., TiMet RNA timeseries data and starting models
Abstract
Authors: Karl Fogelmark, Carl Troein
Date Published: 17th Jul 2014
Publication Type: Journal
DOI: 10.1371/journal.pcbi.1003705
Citation: PLoS Comput Biol 10(7):e1003705
Abstract (Expand)
Authors: A. Pokhilko, A. P. Fernandez, K. D. Edwards, M. M. Southern, K. J. Halliday, A. J. Millar
Date Published: 6th Mar 2012
Publication Type: Not specified
PubMed ID: 22395476
Citation: Mol Syst Biol. 2012 Mar 6;8:574. doi: 10.1038/msb.2012.6.