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).
Web page: http://www.synthsys.ed.ac.uk
Funding details:Data management activity in SynthSys was funded by BBSRC award ROBuST (BB/F005237), EU FP7 Collaborative Project TiMet (award 245143) and the UK Centre for Mammalian Synthetic Biology (award BB/M018040/1 from BBSRC, EPSRC and MRC).
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- People (22)
- Projects (6)
- Institutions (6)
- Investigations (22+5)
- Studies (113+15)
- Assays (176+23)
- Data files (199+68)
- Models (161+91)
- Publications (31)
- Presentations (3+4)
- Events (3+1)
- Documents (36+2)
Projects: POP - the Parameter Optimisation Problem
Institutions: University of Exeter
https://orcid.org/0000-0002-9320-5958Projects: Millar group, TiMet
Institutions: University of Edinburgh
https://orcid.org/0000-0002-9258-583XProjects: Millar group
Institutions: University of Edinburgh
Projects: PlaSMo model repository
Institutions: University of Edinburgh
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: Systo models, PlaSMo model repository, Agro-ecological modelling
Institutions: University of Edinburgh
Projects: PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development
Institutions: University of Edinburgh
https://orcid.org/0000-0003-0737-2408Expertise: arabidopsis thaliana, caenorhabditis elegans, circadian rhythms, chronobiology, Transcriptomics, splicing, alternative splicing, R, photobiology, plant architecture, leaf development
Tools: Molecular Biology, Molecular biology techniques (RNA/DNA/Protein), R, Systems Biology, Transcriptomics, Bioinformatics, Databases, Genetics, Plant biology, C. elegans biology
Projects: PlaSMo model repository
Institutions: University of Edinburgh
Projects: 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/0000-0002-7975-5013What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.
Our aims
To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...
Programme: SynthSys
Public web page: Not specified
Organisms: Arabidopsis thaliana, Ostreococcus tauri
Research programme in the Takato Imaizumi lab, with multiple collaborators. Published in Song et al. Nature Plants 2018; Kinmonth-Schultz et al., in silico Plant 2019.
Programme: SynthSys
Public web page: https://faculty.washington.edu/takato/
Organisms: Arabidopsis thaliana
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
For plants, light is a signal that carries information about the environment, and a source of energy for photosynthesis. PHYTOCAL focuses on the interaction between phytochrome signalling and photosynthesis, and seeks to understand fundamental processes that make carbon (C) and nitrogen (N) resources available for plant growth. These unexplored connections underlie biomass production and plasticity, which contribute significantly to yield variability in the field.
Programme: SynthSys
Public web page: http://hallidaylab.bio.ed.ac.uk/node/1
Organisms: Arabidopsis thaliana, Brassica rapa
EPSRC project with Exeter, SynthSys and EPCC
Programme: SynthSys
Public web page: Not specified
Organisms: Arabidopsis thaliana
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Programme: SynthSys
Public web page: http://timing-metabolism.eu/
Organisms: 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 will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.
Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...
Submitter: Andrew Millar
Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...
Snapshots: Snapshot 1
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
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 ...
Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: F2014.1 - PLM_1030, PLM_67v3withTempPulse - PLM_81
Assays: F2014.1 - PLM_1030, version 1, PLM_67v3withTempPulse - PLM_81, version 1
Snapshots: No snapshots
Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.
Submitter: Andrew Millar
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73, Chew_et_al_2014_Framework_Model - PLM_76, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75, Salazar Photoperiodism Model with T6P - PLM_82, Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1, Chew_et_al_2014_Framework_Model - PLM_76, version 1, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75..., Salazar Photoperiodism Model with T6P - PLM_82, version 1, Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
Snapshots: No snapshots
Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Tomasz Zielinski and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Checking upload for andrew - PLM_1040, Plasmo test model1 - PLM_80
Assays: CHecking if all works - PLM_1000, version 111, Checking upload for andrew - PLM_1040, version 1, Plasmo test model1 - PLM_80, version 1, Test created 1552502361596, Test created 1552502791700, Test created 1552503965203, Test created 1552503978484, Test created 1552504117107, Test created 1552504664537, Test created 1552504857803, Test created 1552505193451
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: TiMet 2011 PP interaction network - PLM_56, TiMet 2011 Pollen network - PLM_54, TiMet 2011 Root network - PLM_55, TiMet 2011 flower specific protein detection network - PLM_57, TiMet 2011 seed network - PLM_53, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_58, TiMet 2011 silqueue specific protein detection network - PLM_59
Assays: TiMet 2011 PP interaction network - PLM_56, version 1, TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2, TiMet 2011 Root network - PLM_55, version 1, TiMet 2011 flower specific protein detection network - PLM_57, version 1, TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5..., TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, T2011 Ostreococcus clock, TOC1 act D - PLM_92, T2011 Ostreococcus clock, TOC1 act L - PLM_91, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, T2011 Ostreococcus clock, acc immediate - PLM_83, T2011 Ostreococcus clock, acc on - PLM_84, Troein Ostreococcus clock 1-loop - PLM_7
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1, T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1, T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2, T2011 Ostreococcus clock, acc immediate - PLM_83, version 1, T2011 Ostreococcus clock, acc on - PLM_84, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, Neurospora Circadian Clock 3-variable model - PLM_51, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Assays: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, version 1, Neurospora Circadian Clock 3-variable model - PLM_51, version 1, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: LINTUL_V2 - PLM_42, SUCROS1 - PLM_24
Assays: LINTUL_V2 - PLM_42, version 1, SUCROS1 - PLM_24, version 1
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: External Coincidence Model - PLM_31
Assays: External Coincidence Model - PLM_31, version 1, External Coincidence Model - PLM_31, version 2
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Martin Beaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Central plant metabolism - PLM_61, Glycolysis SBGN - PLM_60, Insulin-like growth factor signaling - PLM_62, Martin test - PLM_65, Neuronal muscle signalling - PLM_63
Assays: Central plant metabolism - PLM_61, version 1, Glycolysis SBGN - PLM_60, version 1, Insulin-like growth factor signaling - PLM_62, version 1, Martin test - PLM_65, version 1, Martin test - PLM_65, version 2, Neuronal muscle signalling - PLM_63, version 1
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: arabidopsis_clock_biopepa - PLM_47
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis_clock_2011 - PLM_43, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, Arabidopsis_clock_extend - PLM_6
Assays: Arabidopsis_clock_2011 - PLM_43, version 1, Arabidopsis_clock_2011 - PLM_43, version 2, Arabidopsis_clock_2011 - PLM_43, version 3, Arabidopsis_clock_2011 - PLM_43, version 4, Arabidopsis_clock_2011 - PLM_43, version 5, Arabidopsis_clock_2011 - PLM_43, version 6, Arabidopsis_clock_2011 - PLM_43, version 7, Arabidopsis_clock_2011 - PLM_43, version 8, Arabidopsis_clock_2011 - PLM_43, version 9, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 1, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 2, Arabidopsis_clock_extend - PLM_6, version 1, Arabidopsis_clock_extend - PLM_6, version 2, Arabidopsis_clock_extend - PLM_6, version 3
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Chris Davey and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: AFRC Wheat 2 evapw submodel - PLM_33, AFRC Wheat 2 jdaydif submodel - PLM_34, AFRC Wheat 2 julday submodel - PLM_35, AFRC Wheat 2 ldim submodel - PLM_36, AFRC Wheat 2 photpd submodel - PLM_37, AFRC Wheat 2 tdays submodel - PLM_38, AFRC Wheat 2 vappres submodel - PLM_39, AFRC Wheat 2 vernal submodel - PLM_40, AFRC Wheat 2 weathr submodel - PLM_41, AFRC Wheat2 dev submodel - PLM_32, AFRCtest2 - PLM_25, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, Miscanmod - PLM_3
Assays: AFRC Wheat 2 evapw submodel - PLM_33, version 1, AFRC Wheat 2 jdaydif submodel - PLM_34, version 1, AFRC Wheat 2 julday submodel - PLM_35, version 1, AFRC Wheat 2 ldim submodel - PLM_36, version 1, AFRC Wheat 2 photpd submodel - PLM_37, version 1, AFRC Wheat 2 tdays submodel - PLM_38, version 1, AFRC Wheat 2 vappres submodel - PLM_39, version 1, AFRC Wheat 2 vernal submodel - PLM_40, version 1, AFRC Wheat 2 weathr submodel - PLM_41, version 1, AFRC Wheat2 dev submodel - PLM_32, version 1, AFRCtest2 - PLM_25, version 1, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, version 1, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1, Miscanmod - PLM_3, version 1
Snapshots: No snapshots
Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: 3PG - PLM_12, CENTURY_Rowe_daily - PLM_22, DALEC - PLM_23, LINTUL - PLM_4, McMurtrie vegetation model - PLM_11, TRIFFID - PLM_5
Assays: 3PG - PLM_12, version 1, CENTURY_Rowe_daily - PLM_22, version 1, DALEC - PLM_23, version 1, LINTUL - PLM_4, version 1, McMurtrie vegetation model - PLM_11, version 1, McMurtrie vegetation model - PLM_11, version 2, TRIFFID - PLM_5, version 1
Snapshots: No snapshots
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Reproducibility tool set
Snapshots: No snapshots
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: promoter binding affinity calculations on the genome based on PBMs and E...
Snapshots: No snapshots
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
Snapshots: No snapshots
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: Uriel Urquiza Garcia
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: Gatway maps of genomic regions of clock genes, Selection of complemented transgenic lines
Snapshots: No snapshots
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
Snapshots: No snapshots
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi...
Snapshots: No snapshots
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
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
Snapshots: No snapshots
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
Snapshots: No snapshots
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
Snapshots: No snapshots
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...
Snapshots: No snapshots
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
Snapshots: No snapshots
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
Snapshots: No snapshots
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
Snapshots: No snapshots
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...
Snapshots: No snapshots
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
Snapshots: No snapshots
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...
Snapshots: No snapshots
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
Snapshots: No snapshots
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
Snapshots: No snapshots
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...
Snapshots: No snapshots
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...
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), Arabidopsis thaliana
SOPs: No SOPs
Data files: TiMet WP1.1a metabolite data, ED-EN in clock mu...
Snapshots: No snapshots
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...
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)
SOPs: No SOPs
Data files: Flowering time in WT vs prr7prr9 (Nakamichi et ...
Snapshots: No snapshots
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...
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)
SOPs: No SOPs
Data files: Hypocotyl lengths in WT vs prr7prr9 across phot...
Snapshots: No snapshots
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...
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), Arabidopsis thaliana
SOPs: No SOPs
Data files: TiMet WP1.1 qRT-PCR LD to LL and DD
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Sensitivity analysis results (.mat file)
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Sensitivity analysis results (.mat file)
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Arabidopsis - starch and the circadian clock, M..., Chew_et_al_2014_Framework_Model version 1, Matl..., Framework Model v2, Modelling circadian regulation of flowering tim...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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...
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
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...
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), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type), Arabidopsis thaliana : prr7-3 (T-DNA insertion PRR7 / slight effects on clock period in LL)
SOPs: No SOPs
Data files: Laurel and Hardy 1 - Experimental data (excel), Laurel and Hardy 1 - experimental data (.mat file)
Snapshots: No snapshots
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 1 - simulation data (.mat file), Laurel and Hardy 1 mean data and simulations
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type), Arabidopsis thaliana : pgm (EMS AT5G51820 / starch deficient)
SOPs: No SOPs
Data files: Laurel and Hardy 2 - Experimental data (excel), Laurel and Hardy 2 - complete data, Laurel and Hardy 2 - experimental data (.mat file)
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana, Arabidopsis thaliana : pgm (EMS AT5G51820 / starch deficient)
SOPs: No SOPs
Data files: Laurel and Hardy 3 - Experimental data (excel), Laurel and Hardy 3 - complete data, Laurel and Hardy 3 - experimental data (.mat file)
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 2 - simulation data (.mat file), Laurel and Hardy 2 mean data and simulations
Snapshots: No snapshots
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 3 - simulation data (.mat file), Laurel and Hardy 3 mean data and simulations
Snapshots: No snapshots
Transcript profiling by microarray in 4, 6, 8, 12 and 18 h photoperiods, originally published in Flis et al, 2016, Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. doi: 10.1111/pce.12754.
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Flis et al, 2016, Supplemental Table S4, Global...
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Proteomics data file submission to PRIDE, PXD00..., Sample description table for Proteomics data fi..., Table EV1 - Quantitative proteomics dataset, Table EV3, Statistical analysis of protein chan...
Snapshots: No snapshots
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset...
Snapshots: No snapshots
These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Translational coincidence modelling - python sc...
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset..., Table EV1 - Quantitative proteomics dataset
Snapshots: No snapshots
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
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Submitter: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: No organisms
SOPs: No SOPs
Data files: Martin et al, 2012, Ostreococcus N15 labelling ...
Snapshots: No snapshots
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
The file contains the matrices that come from the MCMH sampling during the inference process from PBMs
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
The file contains the matrices that come from the MCMH sampling during the inference process from PBMs
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Transformation of RLU into absolute units using a calibration curve of recombinant MBP-NanoLUC-3FLAG-10His
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Plot of linear regresion of calibration curve for inferring number of molecules from NanoLUC biolumienescence in plant extracts
Creators: None
Submitter: Uriel Urquiza Garcia
4 seeds of stable NanoLUC T3 homozygous lines for LHY, PRR7, TOC1, and ELF3 were seeded in 96-well flat white plate that contained 150 µl of ROBUST media and stratified for 2 days at 4ºC. Then plates were incubated in a 2 hours pulse of white light given and transferred to 22 hours darkness at 21 ºC. Then transferred 12L:12D photoperiod for 10 days. On day 10, 50 µl of 1:50 Furimazine:0.05% Triton X-100 added to each well for tracking NanoLUC bioluminescence. A) Measurements using a Tristar plate ...
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
4 seeds of stable NanoLUC T3 homozygous lines for LHY, TOC1 and ELF3 were seeded in 96-well flat white plate that contained 150 µl of ROBUST media and stratified for 2 days at 4ºC. Then a 2 hours pulse of white light given and transferred to 22 hours darkness at 21 ºC. Then transferred 12L:12D photoperiod for 10 days at which 50 µl of 1:50 Furimazine:0.05% Triton X-100 added to each well for tracking NanoLUC bioluminescence. Measurements using a Tristar plate reader were performed automatically ...
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Small data base of clock proteins profiles obtained with western blots by several authors of A. thaliana collected from the literature. This data can be fed into simple models for making prediction of abosute number of protein when combined with RNA data in absolute units. For example the TiMet data set
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Studies: Predicting absolute levels of clock proteins wi...
Assays: Protein level time series
"Samples of plants were collected in pre-weighed 2 ml microfuge tubes (safelock, Eppendorf) with 5 mm stainless steel grinding balls, and flash frozen in liquid nitrogen. The tissue was ground twice at 30Hz for 1 min in a Tissue Lyser (Qiagen). The samples were flash frozen between grinding steps, then placed on ice and 150 μl of BSII buffer was added to protect the samples from proteolysis, without phosphatase inhibitors (Huang et al. 2016). The tube was weighed and further BSII buffer added to ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
"Plates inoculated with Col-0 seed were grown under the same photoperiod conditions to the plants to be analysed. Plant tissue was harvested, making aliquots of 0.4 gFW. MBP-NL3F10H protein was prepared by the method described by Urquiza-Garcia U. and Millar A.J. in Plant Methods 2019. and then quantified by the linearized Bradford assay protocol using both Bovine serum albumin BSA and Ovoalbumin as standards (Ernst & Zor 2010). Then aliquots spiked with purified enzyme to generate a curve ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
This time series were obtained from the literature by perroming rough quantiftification from western blot images. In some cases the data was quantified by the authors and graphs were provided in the publications. In this case we used ImageJ or https://automeris.io/WebPlotDigitizer/
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
This files contains the predicions generated using a simple model of translation, described in the manuscript. This synthetic data was used to rescale U219.3 resulting in U2019.4 and U2020.3 into U2020.4. The .4 models are only resceled for the mass scale of protein and still present the dynamics of the .3 version
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab
Creators: Andrew Millar, Anna Flis, Ronan Sulpice, Mark Stitt
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar... and 1 hidden item
Studies: Construction of Framework Model version 2 (FMv2) and 1 hidden item
Assays: TiMet WP1.1a Metabolite analysis of clock mutants and 1 hidden item
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on days ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, study Laurel & Hardy 3
Assays: FMv2 simulation
Excel workbook with included Read.Me sheet, including FW and DW biomass data derived from files linked elsewhere; a compilation of the rosette area and gas exchange data for every plant measured of the Col, lsf1 and prr7prr9 genotypes; statistical analysis across the experiments; and charts of the compiled data, some of which are presented as figure panels in the 2022 versions.
Creators: Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Parameters rescaled and scaling factors set to 1
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
This is the scaled version of U2020.4 in sbml file. It already contains the scaling factors
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
Paramters rescaled and scaling factors set to 1
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
Paramteres rescaled and scaling factors set to 1
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Absolute units for proteins in Arabidopsis cloc...
Parameters rescaled and scaling factors set to 1
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
Derived from U2019.3 from Testing the inferred rate of dynamic, gene regulatory network in absolute units
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
Sbml version of U2019.4 with reacaling factors values already incoporated in the model. This was generated autmatically using tellurium python package
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
This file was derived from U2020.3 by introducing the scalig factors in the required locations in the model. This files is used then for numerically rescaling the model for matching synthetic protein data.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units for proteins in Arabidopsis cloc...
A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2". The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication. Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the ...
Creators: Andrew Millar, Daniel Seaton
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Construction of Framework Model version 2 (FMv2)
Assays: Composition of FMv2
Matlab model (could not be represented in SBML) from publication with abstract: Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. ...
Creators: Andrew Millar, Daniel Seaton
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Construction of Framework Model version 2 (FMv2)
Assays: Composition of FMv2
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
Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2020.2, fitted to the TiMet RNA data for wild-type and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wild-type and clock mutants, in absolute units.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model written in Antimony human-readable language and then translate into SBML using Tellurium
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: P2011.1.2
Model written in Antimony human-readable language, Model used in Pokhilko et al 2012
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: P2011.1.2
autogenerated equation listing from the SBML of U2020.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
autogenerated equation listing from the SBML of U2019.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Abstract (Expand)
Authors: Uriel Urquiza-García, Nacho Molina, Karen J. Halliday, Andrew J. Millar
Date Published: 3rd Sep 2024
Publication Type: Journal
DOI: 10.1101/2024.09.03.609973
Citation: biorxiv;2024.09.03.609973v1,[Preprint]
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D Seaton, Virginie Mengin, Anna Flis, Sam T Mugford, Gavin M George, Michael Moulin, Alastair Hume, Samuel C Zeeman, Teresa B Fitzpatrick, Alison M Smith, Mark Stitt, Andrew J Millar
Date Published: 1st Jul 2022
Publication Type: Journal
DOI: 10.1093/insilicoplants/diac010
Citation: in silico Plants 4(2),diac010
Abstract (Expand)
Authors: Uriel Urquiza Garcia, Andrew J Millar
Date Published: 5th Aug 2021
Publication Type: Journal
DOI: 10.1093/insilicoplants/diab022
Citation:
Abstract (Expand)
Authors: Uriel Urquiza-Garcia, Andrew J Millar
Date Published: 20th Mar 2021
Publication Type: Tech report
DOI: 10.1101/2021.03.18.436071
Citation: biorxiv;2021.03.18.436071v1,[Preprint]
Abstract (Expand)
Authors: Uriel Urquiza-García, Andrew J. Millar
Date Published: 1st Dec 2019
Publication Type: Journal
DOI: 10.1186/s13007-019-0454-4
Citation: Plant Methods 15(1),68
Abstract (Expand)
Authors: Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim
Date Published: 2019
Publication Type: Journal
DOI: 10.1093/insilicoplants/diz006
Citation: in silico Plants 1(1),diz006
Abstract (Expand)
Authors: Y. H. Song, A. Kubota, M. S. Kwon, M. F. Covington, N. Lee, E. R. Taagen, D. Laboy Cintron, D. Y. Hwang, R. Akiyama, S. K. Hodge, H. Huang, N. H. Nguyen, D. A. Nusinow, A. J. Millar, K. K. Shimizu, T. Imaizumi
Date Published: 27th Sep 2018
Publication Type: Not specified
PubMed ID: 30250277
Citation: Nat Plants. 2018 Oct;4(10):824-835. doi: 10.1038/s41477-018-0253-3. Epub 2018 Sep 24.
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Alison M. Smith, Mark Stitt, Andrew J Millar
Date Published: 6th Feb 2017
Publication Type: Tech report
DOI: 10.1101/105437
Citation: biorxiv;105437v1,[Preprint]
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar
Date Published: 6th Feb 2017
Publication Type: Tech report
DOI: 10.1101/105437
Citation: biorxiv;105437v2,[Preprint]
Abstract (Expand)
Authors: Deyue Yang, Daniel D. Seaton, Johanna Krahmer, Karen J. Halliday
Date Published: 5th Jul 2016
Publication Type: Not specified
Citation: Proc Natl Acad Sci USA 113(27) : 7667
Abstract (Expand)
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.
Abstract (Expand)
Authors: D. D. Seaton, R. W. Smith, Y. H. Song, D. R. MacGregor, K. Stewart, G. Steel, J. Foreman, S. Penfield, T. Imaizumi, A. J. Millar, K. J. Halliday
Date Published: 21st Jan 2015
Publication Type: Not specified
PubMed ID: 25600997
Citation: Mol Syst Biol. 2015 Jan 19;11(1):776. doi: 10.15252/msb.20145766.
Abstract (Expand)
Authors: Y. H. Chew, B. Wenden, A. Flis, V. Mengin, J. Taylor, C. L. Davey, C. Tindal, H. Thomas, H. J. Ougham, P. de Reffye, M. Stitt, M. Williams, R. Muetzelfeldt, K. J. Halliday, A. J. Millar
Date Published: 10th Sep 2014
Publication Type: Not specified
PubMed ID: 25197087
Citation: Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4127-36. doi: 10.1073/pnas.1410238111. Epub 2014 Sep 2.
Abstract
Authors: Karl Fogelmark, Carl Troein
Date Published: 17th Jul 2014
Publication Type: Not specified
DOI: 10.1371/journal.pcbi.1003705
Citation: PLoS Comput Biol 10(7) : e1003705
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: D. D. Seaton, O. Ebenhoh, A. J. Millar, A. Pokhilko
Date Published: 18th Dec 2013
Publication Type: Not specified
PubMed ID: 24335560
Citation: J R Soc Interface. 2013 Dec 11;11(91):20130979. doi: 10.1098/rsif.2013.0979. Print 2014 Feb 6.
Abstract (Expand)
Authors: B. Wenden, D. L. Toner, S. K. Hodge, R. Grima, A. J. Millar
Date Published: 13th Apr 2012
Publication Type: Not specified
PubMed ID: 22496591
Citation: Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6757-62. doi: 10.1073/pnas.1118814109. Epub 2012 Apr 10.
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.
Abstract (Expand)
Authors: Y. Niwa, T. Yamashino, T. Mizuno
Date Published: 24th Feb 2009
Publication Type: Not specified
PubMed ID: 19233867
Citation: Plant Cell Physiol. 2009 Apr;50(4):838-54. doi: 10.1093/pcp/pcp028. Epub 2009 Feb 20.
Abstract (Expand)
Authors: N. Nakamichi, M. Kita, K. Niinuma, S. Ito, T. Yamashino, T. Mizoguchi, T. Mizuno
Date Published: 17th May 2007
Publication Type: Not specified
PubMed ID: 17504813
Citation: Plant Cell Physiol. 2007 Jun;48(6):822-32. Epub 2007 May 15.
ZIP file of Andrew Millar's pictures showing the growth location and setup on 8th June 2016, for plants that were later harvested at the summer solstice in 2016. Location was at the South edge of King's Buildings campus, outside the shelter belt of trees (so they did not shade the plot). The plot is surrounded by access fencing that also cuts some of the wind, established by UoE greenhouse staff led by Dr. Sophie Haupt. The plants were set up and grown by Sarah Hodge, under a light shade of 4 ...
Creators: Andrew Millar, Sarah Hodge
Submitter: Andrew Millar
The samples that were subsequently harvested for RNA extraction in Takato's summer study; pictures from Young Hun and Akane
Creators: Andrew Millar, Young Hun Song, Akane Kubota
Submitter: Andrew Millar
Outline report of joint research conducted during MSBnet-funded visit of Sanu Shameer to Millar lab
Creators: Andrew Millar, Sanu Shameer, Argyris Zardilis
Submitter: Andrew Millar
Approximate dates of plant growth and harvesting by Sarah Hodge and Andrew Millar, University of Edinburgh
Country: United Kingdom
City: Edinburgh
This is just a placeholder, to be edited
Start Date: 1st Jun 2016
End Date: Not specified
Event Website: Not specified
Country: Switzerland
City: Zurich
Approximate dates of plant growth and harvesting by Imaizumi lab, University of Washington in Seattle
Start Date: 1st Jun 2014
End Date: 1st Jul 2017
Event Website: Not specified
Country: United States
City: Seattle
Construct fof TOC1 for comparision with NanoLUC
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the elf3-2 CCA1p:LUC for rescuing elf3-2 mutation. In this particular case the plants selected were based on hypocotyl length. Based on the data of LUX in which we observed that rhytmicity was rescued in all lines, hypocotyl elongation varied between lines. Therefore, we used hypocotyl length for assesing complementation
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Donor plasmid for Gatway cloning
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Donor plasmid for Gatway cloning
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the cca1-1/lhy-1p:LUC for rescuing cca1-1 mutation.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the cca1-11/lhy-1 CCA1p:LUC for rescuing lhy-1 mutation.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the cca1-1/lhy-1p:LUC for rescuing lhy-11 mutation. This was an alternative to NanoLUC and also for testing the behaviour of LHY.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the prr9/7-9 CCR2:LUC for rescuing prr7-9 mutation.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector for transformation with Agro. This construct was intended for comparision with NanoLUC
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Binary vector used for transforming with Agro ABI the toc1-2 CCA1p:LUC for rescuing the toc1-2 mutant.
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
List of python packages for reproducing the modelling and data analysis results
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Studies: Reproducibility documentation
Assays: Python packages
Donor plasmid for Gatway cloning for CCA1 genomic region
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Donor plasmid for Gatway cloning
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Donor plasmid for Gatway cloning
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units for proteins in Arabidopsis cloc...
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Jupyter notebook that contains the linear regression for inferring numnber of molecules from NanoLUC biolumiescent data in plant extracts using as calibration curve recombinant MBP-NanoLUC-3FLAG-10His
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Documents the model paramter rescaling and set the scaling factors to 1
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia