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Details about this organism
Synonyms (2)thale-cress, mouse-ear cress
Definitions (0)
None defined
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Strain details
Name | Provider name | Provider's strain ID | Genotypes | Phenotypes | Synonym | Comments | Based on |
---|---|---|---|---|---|---|---|
Landsberg (erecta) | Not specified | Not specified | null ERECTA | short, robust inflorescence | La(er) | Originally selected by George Redei in Columbia, Missouri, following X-ray mutagenesis. Used as parent line for many genetic studies by Maarten Koorneef in the Netherlands, and others in 1990's-2000's. | Not specified |
Arabidopsis accession Fei-0 | Dr. Ronan Sulpice from Max Planck Institute for Molecular Plant Physiology, Potsdam - Golm, Germany | Fei-0 | wild-type | wild-type | Fei-0 | Accession collected in Santa Maria da Feira village (Portugal) | Not specified |
Pro35S:MIR156 transgenic Arabidopsis | European Arabidopsis Stock Centre (NASC) | NASC ID: N9952 | wild-type | wild-type | Pro35S:MIR15 | From NASC website: Transgenic plants generated by floral dipping method. The homozygous plants are screened in T3. Donation Date: 2010-07-23 Donated by: Max-Planck-Institute for Developmental Biology, Germany: Detlef Weigel lab | Col-0 wild type |
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End date: 30th Nov 2021
Organisms: Arabidopsis thaliana
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What 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
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Programme: SynthSys
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Organisms: Arabidopsis thaliana, Ostreococcus tauri
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Organisms: Arabidopsis thaliana
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Public web page: http://www.amillar.org
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Organisms: Arabidopsis thaliana
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015.
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Programme: SynthSys
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Organisms: Arabidopsis thaliana, Ostreococcus tauri
The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
ZucAt - Sucrose (from german Zucker) translocation in Arabidopsis thaliana. Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the
...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Arabidopsis thaliana
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.
Investigation: Temperature effects on Arabidopsis floral induc...
Study: Construction of the Framework Model v1.5
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: framework model v1_5
SOPs: No SOPs
Data files: No Data files
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Photoperiod-specific proteome data for Arabidopsis
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...
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
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis clock models P2011.1.2 and P2011.2....
Organisms: Arabidopsis thaliana
Models: Arabidopsis clock model P2011.2.1 - PLM_71, ver..., Arabidopsis clock model P2011.2.1 - PLM_71, ver...
SOPs: No SOPs
Data files: SBSI output from optimisation 26-30 July 2013, ..., Unpacked SBSI optimisation results, PLM_71_ 2
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
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis clock models P2011.1.2 and P2011.2....
Organisms: Arabidopsis thaliana
Models: Arabidopsis clock model P2011.1.2 - PLM_71, ver..., Arabidopsis clock model P2011.1.2 - PLM_71, ver...
SOPs: No SOPs
Data files: No Data files
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
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis_clock_P2011 - PLM_64
Organisms: Arabidopsis thaliana
Models: Arabidopsis_clock_P2011 - PLM_64, version 3, SI..., Arabidopsis_clock_P2011 - PLM_64, version 3, SU...
SOPs: No SOPs
Data files: Copasi file corresponding to PLM_64 version 3, ..., Fig. 1, outline of P2011 model, with P2010 inse..., Fig. 8, cartoon illustrating repressilator stru..., Matlab version of P2011 clock model, PLM_64_ 3, ODE file for Matlab version of P2011 clock mode...
Data for Figure 2I-2K in Chew et al. PNAS 2014.
Experimental conditions: ∼21.3 °C; 12:12-h light/dark cycle; light intensity, 110 μmol·m−2·s−1;mean daytime CO2 level, 375 ppm. The error bars show the SEs of five plants
Further detail on the experimental conditions is contained in the public record on the BioDare resource, link to follow
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of Col-0 accession i...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Biomass of Col-0 Arabidopsis rosette and indivi...
Data for Figure 3G and Supplementary Figure 4, including gas exchange measurements and photo of the experimental setup. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.
These data were acquired in a separate experiment from the biomass, in March 2013. Replication of the earlier biomass study was imperfect, as some plants became a little dry when watering was controlled to reduce moss growth. Sufficient plants grew strongly to measure
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana : Arabidopsis accession Fei-0 (wild-type / wild-type), Arabidopsis thaliana
SOPs: No SOPs
Data files: No Data files
Data for Figure 3G and Supplementary Figure 4, including gas exchange measurements and photo of the experimental setup. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.
These data were acquired in a separate experiment from the biomass, in March 2013. Replication of the earlier biomass study was imperfect, as some plants became a little dry when watering was controlled to reduce moss growth. Sufficient plants grew strongly to measure
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana : Arabidopsis accession Fei-0 (wild-type / wild-type), Arabidopsis thaliana
SOPs: No SOPs
Data files: No Data files
Data for Figure 3A-3F and Supplementary Figures 2, 3, and 6, including leaf number, biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.
These data were acquired in June 2012.
Experimental conditions: ~22C constant temperature; 12:12-h light/dark cycle; light intensity = 130 μmol·m−2·s−1; average daytime CO2 concentration = 375 ppm. 10 plants per genotype per
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana, Arabidopsis thaliana : Arabidopsis accession Fei-0 (wild-type / wild-type)
SOPs: No SOPs
Data files: Biomass of Fei-0 Arabidopsis rosette and leaves, Biomass of Ler Arabidopsis rosette and individ..., Data images of Arabidopsis Fei-0 and Ler plants..., Leaf number in fei-0 and Ler Arabidopsis rosettes
Data for Figure 3A-3F and Supplementary Figures 2, 3, and 6, including leaf number, biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.
These data were acquired in June 2012.
Experimental conditions: ~22C constant temperature; 12:12-h light/dark cycle; light intensity = 130 μmol·m−2·s−1; average daytime CO2 concentration = 375 ppm. 10 plants per genotype per
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana, Arabidopsis thaliana : Arabidopsis accession Fei-0 (wild-type / wild-type)
SOPs: No SOPs
Data files: Biomass of Fei-0 Arabidopsis rosette and leaves, Biomass of Ler Arabidopsis rosette and individ..., Data images of Arabidopsis Fei-0 and Ler plants..., Leaf number in fei-0 and Ler Arabidopsis rosettes
Data for Figures 5D-5F and Supplementary Figure 7B, 7C, including biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive, with two samples as published in 5D. The 'Summary' sheets in the XLSX files include published graphs. Simulation data are included from FMv1.
These data were acquired in April 2014, in a separate experiment from the La(er) and Fei-0.
Experimental conditions: ∼20.7 °C constant temperature; 12h:12h light/dark cycle; light intensity = 100μmol·m−2·s−1;
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : Pro35S:MIR156 transgenic Arabidopsis (wild-type / wild-type)
SOPs: No SOPs
Data files: 35S:miR156 rosette image, Biomass and area of Col-0 and 35S:miR156 Arabid..., Col-0 rosette image, 37 days old, Data images of Arabidopsis Col-0 and 35S:miR156..., Environmental monitoring data for growth room d..., Leaf number in Col-0 and 35S:miR156 Arabidopsis...
Data for Figures 5D-5F and Supplementary Figure 7B, 7C, including biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive, with two samples as published in 5D. The 'Summary' sheets in the XLSX files include published graphs. Simulation data are included from FMv1.
These data were acquired in April 2014, in a separate experiment from the La(er) and Fei-0.
Experimental conditions: ∼20.7 °C constant temperature; 12h:12h light/dark cycle; light intensity = 100μmol·m−2·s−1;
...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of other accessions ...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : Pro35S:MIR156 transgenic Arabidopsis (wild-type / wild-type)
SOPs: No SOPs
Data files: 35S:miR156 rosette image, Biomass and area of Col-0 and 35S:miR156 Arabid..., Col-0 rosette image, 37 days old, Data images of Arabidopsis Col-0 and 35S:miR156..., Environmental monitoring data for growth room d..., Leaf number in Col-0 and 35S:miR156 Arabidopsis...
Data for Figure 4, from the prior publication of Sulpice et al. Mol. Plant 2014: Biomass, net growth and starch levels at end of day and end of night, under light:dark cycles of 4:20, 6:18, 8:16, 12:12 and 18:6 hours.
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Snapshots: No snapshots
Investigation: Arabidopsis Framework Model v1, predicting rose...
Study: Test of FMv1, growth study of Col-0 accession i...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: No Data files
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.
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Modelling and analysis of translational coincid...
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
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Rhythmic and photoperiod-specific transcriptome...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Flis et al, 2016, Supplemental Table S4, Global...
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Rhythmic and photoperiod-specific transcriptome...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset...
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
...
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Snapshots: No snapshots
Investigation: Metabolic analysis of effects of sucrose transl...
Study: Analysis of central carbon and energy metabolis...
Organisms: Arabidopsis thaliana
Models: ZucAt: multi-compartment metabolic model of gro...
SOPs: No SOPs
Data files: ZucAt: FBA constraints for dark conditions, ZucAt: FBA constraints for light conditions, ZucAt: FBA solution of the model under dark gro..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: The compound database, ZucAt: The gene database, ZucAt: The stoichiometric matrix of the model, ZucAt: The transformers database, ZucAt: the model documentation
Submitter: Andrew Millar
Provider Name: European Arabidopsis Stock Centre (NASC)
Provider's strain ID: NASC ID: N9952
Organism: Arabidopsis thaliana
Genotypes: wild-type
Phenotypes: wild-type
Comment: From NASC website: Transgenic plants generated by floral dipping method. The homozygous plants are screened in T3. Donation Date: 2010-07-23 Donated by: Max-Planck-Institute for Developmental Biology, Germany: Detlef Weigel lab
Submitter: Andrew Millar
Provider Name: Dr. Ronan Sulpice from Max Planck Institute for Molecular Plant Physiology, Potsdam - Golm, Germany
Provider's strain ID: Fei-0
Organism: Arabidopsis thaliana
Genotypes: wild-type
Phenotypes: wild-type
Comment: Accession collected in Santa Maria da Feira village (Portugal)
Submitter: Andrew Millar
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Arabidopsis thaliana
Genotypes: null ERECTA
Phenotypes: short, robust inflorescence
Comment: Originally selected by George Redei in Columbia, Missouri, following X-ray mutagenesis. Used as parent line for many genetic studies by Maarten Koorneef in the Netherlands, and others in 1990's-2000's.
Model associated with the following:
Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006
Creator: Hannah Kinmonth-Schultz
Submitter: Hannah Kinmonth-Schultz
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Arabidopsis thaliana
Investigations: Temperature effects on Arabidopsis floral induc...
Studies: Construction of the Framework Model v1.5
Modelling analyses: Composition of Framework Model FMv1.5
Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).
The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model:
Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was
...
Creators: Daniel Seaton, Yin Hoon Chew, Andrew Millar
Submitter: Daniel Seaton
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in Arabid...
Studies: 1 hidden item
Modelling analyses: 1 hidden item
Simplified model file for PLaSMo accession ID PLM_71, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.2.1 - PLM_71, ver...
Originally submitted model file for PLaSMo accession ID PLM_71, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.2.1 - PLM_71, ver...
Simplified model file for PLaSMo accession ID PLM_71, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.1.2 - PLM_71, ver...
Originally submitted model file for PLaSMo accession ID PLM_71, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.1.2 - PLM_71, ver...
Originally submitted model file for PLaSMo accession ID PLM_1041, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock model P2011.3.1 - PLM_1041
Modelling analyses: Arabidopsis clock model P2011.3.1 - PLM_1041, v...
Simplified model file for PLaSMo accession ID PLM_1041, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock model P2011.3.1 - PLM_1041
Modelling analyses: Arabidopsis clock model P2011.3.1 - PLM_1041, v...
Arabidopsis clock model P2011.6.1 SBML imported into Copasi 4.8 and saved as native Copasi file.
Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock model P2011.6.1 - PLM_1044
Modelling analyses: Arabidopsis clock model P2011.6.1 - PLM_1044, v...
The P2011.3.1 SBML model imported into Copasi v4.8, saved as native Copasi file
Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis clock model P2011.3.1 - PLM_1041
Modelling analyses: Arabidopsis clock model P2011.3.1 - PLM_1041, v...
Originally submitted model file for PLaSMo accession ID PLM_73, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Existing models that were re-factored and integ...
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73
Modelling analyses: Chew_et_al_2012_Photothermal_Model - PLM_73, ve...
Originally submitted model file for PLaSMo accession ID PLM_75, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Existing models that were re-factored and integ...
Studies: Part_of_Christophe_et_al_2008_Functional_Struct...
Modelling analyses: Part_of_Christophe_et_al_2008_Functional_Struct...
Originally submitted model file for PLaSMo accession ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: Simile XML v3
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Existing models that were re-factored and integ...
Studies: Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Modelling analyses: Salazar_et_al_2009_Photoperiodism_Model - PLM_7...
Originally submitted model file for PLaSMo accession ID PLM_76, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Existing models that were re-factored and integ...
Studies: Chew_et_al_2014_Framework_Model - PLM_76
Modelling analyses: Chew_et_al_2014_Framework_Model - PLM_76, versi...
This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.
The FMv1 links the following sub-models:
1. Arabidopsis leaf carbohydrate model (Rasse and
...
Creators: Andrew Millar, Yin Hoon Chew
Submitter: Andrew Millar
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Arabidopsis thaliana
Investigations: Arabidopsis Framework Model v1, predicting rose..., Prediction and analysis of phenotypes in Arabid... and 1 hidden item
Studies: Construction of Framework Model v1 and 2 hidden items
Modelling analyses: Arabidopsis Framework Model v1, Matlab and Simi... and 2 hidden items
Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.
Creator: Andrew Millar
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in Arabid...
Studies: 1 hidden item
Modelling analyses: 1 hidden item
This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.
http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1
Creator: Andrew Millar
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in Arabid... and 1 hidden item
Studies: 2 hidden items
Modelling analyses: 2 hidden items
Creator: Daniel Seaton
Submitter: Daniel Seaton
Model type: Algebraic equations
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Modelling and analysis of translational coincid...
Modelling analyses: Translational coincidence model
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Modelling analyses: Flux Balance Analysis of multi-compartment meta... and 1 hidden item
Abstract (Expand)
Authors: Maksim Zakhartsev, Irina Medvedeva, Yury Orlov, Ilya Akberdin, Olga Krebs, Waltraud X. Schulze
Date Published: 1st Dec 2016
Publication Type: Journal
DOI: 10.1186/s12870-016-0868-3
Citation: BMC Plant Biol 16(1),262
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 (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: 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.
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: No date defined
Publication Type: Not specified
DOI: 10.1101/105437
Citation: Linking circadian time to growth rate quantitatively via carbon metabolism
Abstract (Expand)
Authors: Daniel Seaton, Alexander Graf, Katja Baerenfaller, Mark Stitt, Andrew Millar, Wilhelm Gruissem
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/182071
Citation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Abstract (Expand)
Authors: A. Flis, R. Sulpice, D. D. Seaton, A. A. Ivakov, M. Liput, C. Abel, A. J. Millar, M. Stitt
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 27075884
Citation: Plant Cell Environ. 2016 Sep;39(9):1955-81. doi: 10.1111/pce.12754. Epub 2016 Jul 15.