Assays
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Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Biomass and metabolites in Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA)
Submitter: Andrew Millar
Assay type: Organism or Strain Characteristics
Technology type: Cultivation experiment
Investigation: Prediction and analysis of phenotypes in the Ar...
Luciferase reporter gene assay for circadian period of seedlings in constant light, for Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA). Supplementary Figure 11f in Chew et al., _in Silico _Plants.
Raw and processed data, together with circadian period analysis and summary statistics, are available from BioDare.ed.ac.uk: choose https://biodare.ed.ac.uk/experiment ("Browse Public Resources" on the Login screen), then you can link to https://biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3838, ...
Submitter: Andrew Millar
Assay type: Transcriptional reporter gene
Technology type: Imaging
Investigation: Prediction and analysis of phenotypes in the Ar...
Biomass, leaf number and gas exchange data for Col0 (WT), prr7prr9, and lsf1, compiled from four studies: L&H1-3 and the 'no GA' controls of Gibberellins 1.
Submitter: Andrew Millar
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col.
In this study, 14CO2 labelling was used to test the rate of carbon assimilation in the dark at the end of the subjective night (starting about ZT21), which is indicative of PEPC activity in forming malate, and the subsequent partitioning of this labelled C into various cellular fractions. The short-period ...
Submitter: Andrew Millar
Assay type: Metabolite Profiling
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col.
In this study, thiamine vitamers were quantified to test whether the essential cofactor TDP had altered enzyme activities to affect the malate and fumarate levels, using existing plant samples harvested from am earlier L&H study.
Submitter: Andrew Millar
Assay type: Metabolite Profiling
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and pgm at days 29 and 35, presented in the preprint/publication, with most data also for Col and lhycca1 at days 21/22/23, not analysed further.
We suggest that the lower carbon assimilation rate measured in lhycca1 (see gas exchange data) might allow a calibirated simulation in the FMv2 model in future to incorporate the indirect effects of nightly carbon starvation in this genotype ...
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
effects of 1% increase in each parameter, more detailed analysis of water content
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
correlations of starch mobilisation and fresh weight under single parameter changes
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
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...
Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and lsf1 (presented in the preprint/paper) and pgm (not analysed further).
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Simulation data from FMv2 calibrated for experiment L&H2, an experiment run at 18.5C instead of the 20.5C of the replicate and related studies. The Excel file includes the mean and SD of the relevant experimental data, and the figure panels.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Metabolite analysis in clock mutants: Col-0 parent and mutants gi-201, toc1-101 and prr7prr9; WS parent and lhy/cca1 double mutant. Plants grown in Golm and harvested at End of Day and End of Night, , assays 22 major metabolites. More detail on TiMet wiki if required. Heteroscedastic t-tests to highlight most significant changes, without multiple-testing correction.
Submitter: Andrew Millar
Assay type: Metabolite Concentration
Technology type: Chromatography
Investigation: Prediction and analysis of phenotypes in the Ar...
RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL
Submitter: Andrew Millar
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Prediction and analysis of phenotypes in the Ar...
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...
Biomass, leaf number and metabolites in Col0 (WT), prr7, prr7prr9, and lsf1. Metabolite data from plants after 28 days of growth were analysed most (27 days 'end of night', 28 days 'end of day' and 'end of night'). The data file also includes data from 21 days of growth ('end of day' and 'end of night'), which is useful for comparison to early-flowering plants not tested here, such as the lhycca1 double mutant, that flower before 28 days, altering their physiology.
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
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...
P2011.1.2 written in Antimony and converted in SBML using python package Tellurium. Parameters values correspond to P2011.1.2
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Collection of clock models that rescale transcript variables to account for absolute units. The relationship between models is summarised in the attached 'model evolution' document and in more detail in the linked publications (preprint version linked in the Snapshot; publication Urquiza and Millar, In Silico Plants 2021 did not have a DOI when Snapshot was created).
Each model is presented three times,
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- without a light:dark cycle,
-
- with an ISSF (Adams et al. JBR 2012) that is set up for ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Gene Regulatory Network
Investigation: Absolute units in Arabidopsis clock models up t...
This section contains the links to the tools used for reproducing the computational results presented in U2019. This is required because SloppyCell is under the risk of becoming rotting code. Using Docker we can assure some persistence for the computational environment that allows to run SloppyCell.
The associated git repository can be found in https://github.com/jurquiza/Urquiza2019a.git which can be cloned.
The docker image can either be pulled from the docker hub site
docker pull ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Model files for FMv1.5. The model is based on FMv1 of Chew et al. PNAS 2014, which is also in FAIRDOMHub and linked to the Model record as an 'Attribution'. FMv1 was extended in this work by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Temperature effects on Arabidopsis floral induc...
Plant material The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for ...
Submitter: Daniel Seaton
Assay type: Protein Quantification
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)