Assays
What is an Assay?Filters
DALEC (Data Assimilation Linked Ecosystem Carbon) represents the C cycle with a simple box model of pools connected via fluxes. There are five pools: C content of foliage (Cf); woody stems and coarse roots (Cw) and fine roots (Cr); and of fresh leaf and fine root litter (Clitter) and soil organic matter (SOM) plus WD (CSOM/WD). The fluxes among pools are based on the following assumptions: All C fixed during a day is either expended in autotrophic respiration or else allocated to one of three ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Muetzelfeldt, Robert
Study: DALEC - PLM_23
Excel file with metablite profiles after 24 h incubation with different ratios of 11HSDB1 and AKR1C3.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...
Submitter: Ziva Ramsak
Assay type: Degradome-Seq
Technology type: Next generation sequencing
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Proton fluxes ensue a change in the membrane potential to which the potassium uptake responds. The membrane potential changes depend on the extrusion of protons, buffering capacities of the media and experimental parametes.
Submitter: Falko Krause
Biological problem addressed: Model Analysis Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Kinetic properties of Trk
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
Mutants with a linear respiratory chain consisting of NADH Dehydrogenase II and one of the terminal oxidases cytochrom bo, cytochrome bd I or cytochrome bd II were growth in chemostats with defined oxygen supply. The amounts of biomass formed and of acetate and formate produced were determined.
Submitter: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Chemostat Measurement
Investigation: Analysis of Escherichia coli with linear electr...
Determination of essential amino acids for Streptococcus pyogenes
Submitter: Araz Zeyniyev
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Amino acid metabolism of four LAB species: Stre...
The task of this assay is to determine the impact of oxygen availability on the concentrations of metabolites from different central metabolic pathways. The focus lies on metabolites connected to glycolysis, tri-carbon-acid-cycle and energy metabolism. All strains have been cultured and analysed according to the SOPs listed below
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Steady state studies for different oxygen avail...
This assay describes the determination of concentrations and ratio of metabolites of adenine nucleotides (NAD and NADH). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Initial Rate Experiment
Investigation: Steady state studies for different oxygen avail...
This assay describes the determination of concentrations and ratio of metabolites of ubiquinones (oxidised and reduced form). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: HPLC
Investigation: Steady state studies for different oxygen avail...
Analytical methods and computational analyses (regression, fitting) will be employed to find properties of the Trk system under different external conditions.
Submitter: Falko Krause
Biological problem addressed: Model Analysis Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Kinetic properties of Trk
Mutants with linear respiratory chains were grown under SUMO chemostat conditions at different defined aerobiosis levels. The ArcA phoshorylation state as determined.
Submitter: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Gel Electrophoresis
Investigation: Analysis of Escherichia coli with linear electr...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MetNet
Differential expression analysis (using R package edgeR) on liver gene expression between salmon with all four fads2 genes knockout, only fads2d6b & fads2d6c knockout and wildtype. All salmon was given either a low-PUFA diet or a high-PUFA diet
Submitter: Yang Jin
Biological problem addressed: Model Analysis Type
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Study: FADS Knockout
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Data digitized from publication.
Akinyinka2000 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Amchin1999 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Blanchard1983a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Haller2002 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Healy1991 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Hetzler1990 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Jeppesen1996 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Kakuda2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Kaplan1997 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Magnusson2008 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Oh2012 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Perera2011 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Spigset1999a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Tanaka2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Description of observed phenotypic variables in the MOA investigation.
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Imaging
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Homogeneity of the Gre2p samples in HEPES and PBS Buffer before and after different treatments.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Homogeneity of the Gre2p samples in KPi Buffer before and after different treatments, including different amounts of tween-20 in the buffer (0.01, 0.1, 1.0%).
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Homogeneity of the Gre2p samples in KPi Buffer before and after different treatments, including different amounts of BSA in the buffer (7.5 µM and 75 µM).
Submitter: Felix Ott
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Prepared target (parasite PTR1, DHFR) and off-target (human DHFR) protein receptors for docking studies, in part with conserved structural water sets, and the corresponding preparation routine.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms. Molecular Systems Biology 9 Article number: 650 doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Originally ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms. Molecular Systems Biology 9 Article number: 650 doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Version ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
Submitter: Xiaokang Zhang
Biological problem addressed: Metabolic Network
Investigation: 1 hidden item
Study: 1 hidden item
The associated zip files contains all input files and a Jupyter notebook to rerun sampled simmulations, combined simmulations, parameter scan for the model with addition of an oxygin inhibiton of LDH, local- and global-sensitivity analysis and plot simmulation output in various formats. In addition the zip file contains the py36.yaml file that can be used to recreate the model simmulation environment using Anaconda making all simmulations completely reproducable. All information on how to use ...
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model predictions
Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Investigation: Kinetic analysis of metabolic system using tran...
Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, ...
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Kinetic analysis of metabolic system using tran...
Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...