Assays

Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods

Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods

Biomass and metabolites in Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA)

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, ...

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.

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 ...

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.

effects of 1% increase in each parameter, more detailed analysis of water content

correlations of starch mobilisation and fresh weight under single parameter changes

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

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.

RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL

Combination of multiple sub-models to form Framework Model version 2

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.

P2011.1.2 written in Antimony and converted in SBML using python package Tellurium. Parameters values correspond to P2011.1.2

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,

• • without a light:dark cycle,
• • with an ISSF (Adams et al. JBR 2012) that is set up for ...

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 ...

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.

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 ...

Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally ...

The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

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 ...

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 ...

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 ...

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 ...

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 ...

Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.Related PublicationsWilczek et al. (2009). Effects of Genetic Perturbation ...

Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.Related PublicationsWilczek et al. (2009). Effects of Genetic Perturbation ...

Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558

Originally submitted to PLaSMo on 2011-08-12 15:34:00

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...