Assays

1172 Assays visible to you, out of a total of 2144

Arabidopsis Framework Model v1, Matlab and Simile version

Millar group

In future we should split these versions into separate Assays, and link to the four, original component models, when they are imported with the PlaSMo resource into FairdomHub (expected late 2018)

Submitter: Andrew Millar

Biological problem addressed: Model Analysis Type

Investigation: Arabidopsis Framework Model v1, predicting rose...

Study: Construction of Framework Model v1

Organisms: No organisms

Models: Chew_et_al_2014_Framework_Model version 1, Matl...

SOPs: No SOPs

Data files: Supplementary Information on FMv1 model

Snapshots: No snapshots

Created: 22nd Aug 2018 at 11:23, Last updated: 22nd Aug 2018 at 11:28

Growth of Col-0 plants in 5 photoperiods

Millar group

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

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

Snapshots: No snapshots

Created: 22nd Aug 2018 at 10:49, Last updated: 22nd Aug 2018 at 11:17

Biphasic control can provide mutant resistance to stem-cell homeostatic circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 4D: Biphasic control can provide mutant ...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:32

Biphasic control can provide mutant resistance to stem-cell homeostatic circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 4C: Biphasic control can provide mutant ...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:32, Last updated: 31st Jul 2018 at 10:32

Frequency-dependent selection of mutant pancreatic beta cells.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 2: Frequency-dependent selection of muta...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:31

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1G: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:30

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1H: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:29

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1D: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:29

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1C: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:28

Frequency doubling in the cyanobacterial circadian clock

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Martins et al (2016) Molecular Systems Biology

Study: Figure 4B: A minimal mathematical model, contai...

Organisms: No organisms

Models: Frequency doubling in the cyanobacterial circad...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 30th Jul 2018 at 19:17

Frequency doubling in the cyanobacterial circadian clock

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Martins et al (2016) Molecular Systems Biology

Study: Figure 6C and D: The clock-sigC circuit represe...

Organisms: No organisms

Models: Frequency doubling in the cyanobacterial circad...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 30th Jul 2018 at 14:58

gustavsson1-4 models

Yeast glycolytic oscillations

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Sustained glycolytic oscillations in individual...

Organisms: No organisms

Models: gustavsson1-4 models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:38

gustavsson5 model

Yeast glycolytic oscillations

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Allosteric regulation of phosphofructokinase co...

Organisms: No organisms

Models: gustavsson5 model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:18

Metabolomics Master Template

SysMO DB, FAIRDOM, FAIRDOM user meeting

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

Submitter: Katy Wolstencroft

Assay type: Metabolomics

Technology type: Technology Type

Investigation: Creating data sheet template for 'omics data

Study: Creating template for metabolomics data

Organisms: No organisms

SOPs: No SOPs

Data files: Metabolomics Master Excel Template and 1 hidden item

Snapshots: No snapshots

Created: 28th Feb 2012 at 13:33, Last updated: 3rd Mar 2018 at 10:59

Translational coincidence model

Millar group, TiMet

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...

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

Snapshots: No snapshots

Created: 4th Dec 2017 at 21:41, Last updated: 20th Feb 2018 at 22:03

Stitt lab, TiMet photoperiod microarrays

Millar group, TiMet

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...

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...

Snapshots: No snapshots

Created: 4th Dec 2017 at 13:23, Last updated: 20th Feb 2018 at 22:03

Blasing et al, 2005, diurnal microarray in 12L:12D

Millar group, TiMet

No description specified

Submitter: Daniel Seaton

Assay type: Gene Expression Profiling

Technology type: Microarray

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...

Snapshots: No snapshots

Created: 4th Dec 2017 at 21:33, Last updated: 20th Feb 2018 at 22:03

Martin et al, 2012, Ostreococcus N15 labelling proteomics data

Millar group, TiMet

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...

Study: Proteome and translation rate data for the Ostr...

Organisms: No organisms

SOPs: No SOPs

Data files: Martin et al, 2012, Ostreococcus N15 labelling ...

Snapshots: No snapshots

Created: 14th Jan 2018 at 22:30, Last updated: 20th Feb 2018 at 22:03

Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis

Millar group, TiMet

Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.

Submitter: Daniel Seaton

Assay type: Proteomics

Technology type: Mass Spectrometry

Investigation: Photoperiodic control of the Arabidopsis proteo...

Study: Proteome and translation rate data for the Ostr...

Organisms: No organisms

SOPs: No SOPs

Data files: Aryal et al, 2011, metabolic labelling of Cyano...

Snapshots: No snapshots

Created: 14th Jan 2018 at 22:37, Last updated: 20th Feb 2018 at 22:03

Estimation of rates of translation and turnover from proteomics datasets

Millar group, TiMet

Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.

Submitter: Daniel Seaton

Biological problem addressed: Model Analysis Type

Investigation: Photoperiodic control of the Arabidopsis proteo...

Study: Proteome and translation rate data for the Ostr...

Organisms: Ostreococcus tauri

Models: Estimation of translation and turnover - python...

SOPs: No SOPs

Data files: Aryal et al, 2011, metabolic labelling of Cyano..., Calculated rates of protein degradation in Cyan..., Calculated rates of protein degradation in Ostr..., Calculated rates of protein synthesis in the li..., Calculated rates of protein synthesis in the li..., Martin et al, 2012, Ostreococcus N15 labelling ...

Snapshots: No snapshots

Created: 15th Jan 2018 at 07:24, Last updated: 20th Feb 2018 at 22:03

RNAseq

SysMetEx

RNAseq data for L.ferriphilum samples

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Multi -omics reveal lifestyle of acidophile, mi...

Study: Omics_data_analysis

Organisms: No organisms

SOPs: No SOPs

Data files: LF_RNAseq_TPM_continuous, LF_RNAseq_TPM_mineral, LF_RNAseq_rawdata, LF_deseq_comparison, LF_omics_analysis, LF_omics_combined_Table

Snapshots: No snapshots

Created: 19th Jul 2017 at 23:51, Last updated: 8th Nov 2017 at 14:21

Proteomics

SysMetEx

Proteomics data for L.ferriphilum samples (continuous and with mineral)

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Multi -omics reveal lifestyle of acidophile, mi...

Study: Omics_data_analysis

Organisms: No organisms

SOPs: No SOPs

Data files: LF_LFQ_comparison_ttest, LF_omics_analysis, LF_omics_combined_Table, LF_proteomics_LFQs_continuous, LF_proteomics_LFQs_mineral, LF_proteomics_LFQs_mineral_scaled, LF_proteomics_continuous_scaled, LF_proteomics_maxquant_perseus_filtered, LF_proteomics_maxquant_perseus_unfiltered, Perseus workflow t-test, Proteomics data comparing LXX cultures cultivat...

Snapshots: No snapshots

Created: 19th Jul 2017 at 23:59, Last updated: 8th Nov 2017 at 14:21

Genomics

SysMetEx

Genomics data, for L.ferriphilum Sequencing of the genome and functional annotation

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Multi -omics reveal lifestyle of acidophile, mi...

Study: Omics_data_analysis

Organisms: No organisms

SOPs: No SOPs

Data files: Functional_annotation_repository, LF_functional_annotation_gbk, LF_omics_combined_Table, LF_sequencing_data

Snapshots: No snapshots

Created: 20th Jul 2017 at 00:04, Last updated: 8th Nov 2017 at 14:21

Experimental methods

SysMetEx

Collection for experimental SOPs

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Multi -omics reveal lifestyle of acidophile, mi...

Study: Omics_data_analysis

Organisms: No organisms

SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - Bioleaching in flasks (LNU), SOP - RNA/Protein sampling for continuous culture

Data files: No Data files

Snapshots: No snapshots

Created: 20th Jul 2017 at 00:12, Last updated: 8th Nov 2017 at 14:21

PGK 30C data

SulfoSys, SulfoSys - Biotec

Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-30C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK yeast with recycling of ATP, PGK yeast without recycling of ATP

Snapshots: No snapshots

Created: 28th Sep 2017 at 10:08, Last updated: 8th Nov 2017 at 14:21

PGK 70 data

SulfoSys, SulfoSys - Biotec

Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: NMR

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-70C

Organisms: No organisms

SOPs: No SOPs

Data files: Sso PGK (14 ug/ml) in presence of recycling sys..., Sso PGK (28 ug/ml) in presence of recycling sys..., Sso PGK in absence of recycling system, 31P NMR..., Sso PGK in presence of ATP recycling system at ...

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:16, Last updated: 8th Nov 2017 at 14:21

BPG degradation

SulfoSys, SulfoSys - Biotec

BPG degradation at 70C

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: BPG stability

Organisms: No organisms

SOPs: No SOPs

Data files: BPG degradation at 70

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:17, Last updated: 8th Nov 2017 at 14:21

PGK-GAPDH 30

SulfoSys, SulfoSys - Biotec

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-GAPDH 30C & 70C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK-GAPDH 30, 3PG, GAP & BPG, PGK-GAPDH 30, PYR

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:58, Last updated: 8th Nov 2017 at 14:21

PGK-GAPDH 70

SulfoSys, SulfoSys - Biotec

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-GAPDH 30C & 70C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK-GAPDH 70

Snapshots: No snapshots

Created: 28th Sep 2017 at 12:01, Last updated: 8th Nov 2017 at 14:21

Whole genome sequencing (Illumina)

Noisy-Strep

No description specified

Submitter: Jan-Willem Veening

Assay type: Experimental Assay Type

Technology type: Next generation sequencing

Investigation: Chromosome segregation and cell division in Str...

Study: Genome wide marker frequency analysis on new st...

Organisms: No organisms

SOPs: No SOPs

Data files: DCI15, MK453, MK454, Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai...

Snapshots: No snapshots

Created: 19th Jul 2016 at 08:33, Last updated: 8th Nov 2017 at 14:21

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