Assays
What is an Assay?Filters
Kinetic characterisation en mathematical modelling of G3PDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Matthias König
Biological problem addressed: Model Analysis Type
Investigation: MM-PLF: Multiscale modeling for personalized li...
Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Kinetic characterisation en mathematical modelling of GAPDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Metabolic control analysis of glyceraldehyde 3-...
Mathematical model for GAPDH kinetics, saturation with BPG, NADPH, NADP, GAP and Pi
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
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
Investigation: Arabidopsis Framework Model v1, predicting rose...
Submitter: Meina Neumann-Schaal
Assay type: Experimental Assay Type
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Salmonella enterica relies on carbon metabolism...
Analyses of gene expression: qPCR analyses in liver (relative expression) and ovaries (absolute expression).
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Mutant strains with linear electron transport chain were grown in chemostat cultures at different defined aerobiosis levels. Expression of selected genes was determined by Real Time RT-PCR
Submitter: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: qRT-PCR
Investigation: Analysis of Escherichia coli with linear electr...
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: The transition from growing to non-growing Baci...
General sandbox
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: FAIRDOMhub API usage in R
Generic metadata template describing High Content Screening data that conform to the REMBI and ISA specification. LEI-MIHCSME empty template that can serve as basis for filling in metadata. This template was created and modified from templates produced by Leiden University.
Submitter: Rohola Hosseini
Assay type: high content screening
Technology type: Imaging
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO. These templates are generic and non-specific for any particular array platform.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Submitter: Federico Rojas
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Perturbing the biological system: developmental...
This assay is for method development to quantify intra- and extra-cellular metabolites on T. brucei 427 bloodstream form using isotope ratio based MS technique with 13C-labelled E. coli extract
Submitter: Dong-Hyun Kim
Assay type: Metabolite Concentration
Technology type: Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Study: Metabolic flux measurement
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Metabolic network of Enterococcus faecalis including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors
Submitter: Nadine Veith
Biological problem addressed: Metabolic Network
Investigation: Investigation of glycolysis and pyruvate branch...
Metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors
Submitter: Jennifer Levering
Biological problem addressed: Metabolic Network
Investigation: Investigation of glycolysis and pyruvate branch...
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
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model validation
Submitter: Dawie van Niekerk
Biological problem addressed: Validation
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Data for global pH monitoring for precipitation experiments included in the publication: Microbial-induced calcium carbonate precipitation An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution Included data: Calibration data and pH time evolution
Submitter: Jennifer Zehner
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Global sensitivity analysis of a kinetic model to determine the sensitivities for each parameter, over a wide parameter range. We used the elementary effects method.
Submitter: Mark Musters
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
L. lactis was grown in LAB medium or rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.
Submitter: Martijn Bekker
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
S. pyogenes was grown in rich medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.
Submitter: Martijn Bekker
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
SBGN model of glycolysis
Originally submitted to PLaSMo on 2012-03-05 11:43:15
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Beaton, Martin
Study: Glycolysis SBGN - PLM_60
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Cytoscape based analysis and yED based representation of clostridial Reactomes
Submitter: Sebastian Curth
Biological problem addressed: Model Analysis Type
Investigation: Modular Model Building
Study: Reactome Analysis
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
Investigation: Arabidopsis Framework Model v1, predicting rose...
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
Investigation: Arabidopsis Framework Model v1, predicting rose...
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...
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
Investigation: Arabidopsis Framework Model v1, predicting rose...
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glycolytic oscillations in individual isolated ...
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 ...