Studies
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Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: promoter binding affinity calculations on the genome based on PBMs and E...
Files required for reproducibility of computational results. This include Docker file and python packages
Submitter: Uriel Urquiza Garcia
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: Python packages
Clock mutants for lhy-1/cca1-11, prr9/7, toc1, lux-4, elf3-1 were transformed with the genomic regions of the associated clock genes tagged with NanoLUC-3FLAG-10His. The tagged genomic constructs were transformed in the mutants using Agrobcterium ABI strain (kindly donated by Prof. Seth Davis University of York). T3 plants resistant to homozygous for BASTA resistance were phenotyped by luciferase imaging asessing period phenotype or plant architecture. Rescuing lines were then used for performing ...
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: Jupyter notebook Predicting Protein Numbers, Protein level time series, TiMet RNA timeseries data
Modelling and experiments for FMv2 components.
Simulations, parameter sensitivity analysis etc. for FMv2
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Relationship among FMv2 outputs, Sensitivity analysis of FMv2
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Model simulations compared to experimental data from the literature (publications from Mizuno lab are linked), testing the FMv2.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass, leaf number and metabolites, FMv2 simulation
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. New collaborations with the groups of Teresa Fitzpatrick and TiMet partner Samuel Zeeman.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Assimilation and partitioning of 14CO2 at night, Thiamine vitamers
Assorted files prepared during the publication process of the FMv2, its validation and testing, mostly focussed on the Arabidopsis double mutant prr7prr9 and its parent accession Col. Data from other studies that are described separately, and linked by Atribution to the File records under this Study.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Collection of models used in the introduction of absolute units into A. thaliana circadian clock models, with software resources and documentation. The models are inspired by P2011, published in Pokhilko et al 2012. The study contains Assays that link to the P2011 starting model and the models U2019.1 - .3 and U2020.1 - .3. Each model is shared as a human-readable file in the Antimony language and the associated, machine-readable SBML file, which was automatically generated using the SBML export ...
Submitter: Uriel Urquiza Garcia
Investigation: Absolute units in Arabidopsis clock models up t...
Assays: P2011.1.2, Reproducibility tool set, U2019/U2020 models
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...
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
Submitter: BioData SynthSys
Investigation: Urquiza Garcia, Uriel
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 ...
Submitter: BioData SynthSys
Investigation: Urquiza Garcia, Uriel
Assays: F2014.1 - PLM_1030, version 1
Assays for model composition here, in order to share model files; potentially training and validation data in other Studies.
Submitter: Andrew Millar
Investigation: Temperature effects on Arabidopsis floral induc...
This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. Instructions to run the Photoperiodism Model in Simile 1. Save all the files into the same folder. 2. Copy and paste the attached ‘lightfunction.pl’ file in the following folder: Program File > Simile6.0 (or other software version)> Functions 3. Download the ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar Photoperiodism Model with T6P - PLM_82, version 1
This is part of the GreenLab Functional-Structural Plant Model for Arabidopsis published in Christophe et al 2008. This model was re-factored, to facilitate the integration in the Chew et al Framework Model, and it cannot be run as a standalone model. Related PublicationsAngélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75...
This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. Instructions to run the Photothermal Model in Simile 1. Download the Simile file attached or import the XML into Simile: a. File > Import > XML Model Description 2. To run the model: a. Model > Run or click on the ‘Play’ ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1
Submitter: Andrew Millar
Investigation: Arabidopsis flowering in natural long days
Assays: No Assays
The models in this record were published in Flis et al. Royal Society Open Biology 2015. Their original IDs in the PlaSMo resource and IDs in Biomodels are given below. Please select files for download from the 'Related Items' list or the object tree/graph, below. 'SUBMITTED' is the original model version; 'SIMPLIFIED' removes SBML elements that were incompatible with SloppyCell software.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, ...
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
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
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
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., ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2