Assays
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Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Biological problem addressed: Gene Expression
Investigation: The transition from growing to non-growing Baci...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
The experimental data of Midazolam, OH-Midazolam, Caffein, Codeine, Norcodeine, Codein-6Glucuronide, Morphine-3Glucuronide and Morphine was analyzed via a Bayesian uncertainty quantification. An underlying model describing the bolus injection, followed by the exponential decay was written in sbml and a PEtab problem was created. The sampling and ensemble creation was conducted with the python toolbox pyPESTO.
For further details, please take a look at the methods section of the paper.
Submitter: Sebastian Höpfl
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
The experimental data of Midazolam, OH-Midazolam, Caffein, Codeine, Norcodeine, Codein-6Glucuronide, Morphine-3Glucuronide and Morphine was analyzed via a Bayesian uncertainty quantification. An underlying model describing the bolus injection, followed by the exponential decay was written in sbml and a PEtab problem was created. The sampling and ensemble creation was conducted with the python toolbox pyPESTO.
For further details, please take a look at the methods section of the paper.
Submitter: Sebastian Höpfl
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
For analyzing the binding of CcpA-HPrSer46P-complexes to various cre-elements, Surface Plasmon Resonance was used. All operations were carried out on a Biacore X instrument (Biacore, Uppsala, Sweden). Biotinylated cre DNA was coupled on a Neutravidin coated chip in flowcell two, a biotinylated reference DNA in flowcell one. For visualizing only the interactions of the CcpA-HPrSer46P-complex with the cre elements, CcpA was saturated with 50µM HPrSer46P. Titrations were carried out with 5-100nM ...
Submitter: Maike Bartholomae
Assay type: Protein-protein Interaction
Technology type: Surface Plasmon Resonance
Investigation: A dynamic model of the CcpA regulation network
ITC binding (BIND) experiments to determine the binding parameters of HK ((5S,8S)-anti hydroxyketone) to Gre2p in 100 mM KPi Buffer. Experiments failed due to very weak binding and poor solubility of HK in buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiments to determine the binding parameters of NADP+ to Gre2p in 100 mM HEPES Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiments to determine the binding parameters of NADP+ to Gre2p in 100 mM KPi Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiments to determine the binding parameters of NADP+ to Gre2p in 1x PBS Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiments to determine the binding parameters of NADPH to Gre2p in 100 mM HEPES Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiment to determine the binding parameters of NADPH to Gre2p in 100 mM KPi Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiment to determine the binding parameters of NADPH to Gre2p in 1x PBS Buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiment to determine the binding parameters of NADPH to Gre2p in 100 mM KPi Buffer with 0.1% Tween-20 added.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
ITC binding (BIND) experiments to determine the binding parameters of NDK (nitrononane-2,8-dione) to Gre2p in 100 mM KPi Buffer. Experiments failed due to very weak binding and poor solubility of NDK in buffer.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
Motivated by an increasing population and the desire to grow plants more efficiently, attention has turned to the use of Light Emitting Diodes (LEDs) to illuminate plants which are grown indoors. Indoor growing facilities enable closely controlled and mon- itored environmental conditions. More and more of these facilities exchange High Pressure Sodium (HPS) lamps for LED lighting since they provide more efficient lighting and the possibility to control light intensity and quality in order to ...
Submitter: Felix Steimle
Assay type: Experimental Assay Type
Technology type: Chlorophyll Fluorescence Analysis
Investigation: 1 hidden item
S. pyogenes M49 (591), E. faecalis V583, and L. lacis NZ9000 and their isogenic ldh deletion mutants were grown glucose free CDM-LAB medium in BIOLOG phenotype microarray plates PM01 and PM02. With this assay the abilitiy of the strains to grow on 190 different carbon sources was determined in 96 well format.
Submitter: Tomas Fiedler
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
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...
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...
Biomass and metabolites in Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA)
Submitter: Andrew Millar
Assay type: Organism or Strain Characteristics
Technology type: Cultivation experiment
Investigation: Prediction and analysis of phenotypes in the Ar...
Biomass weight 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: Experimental Assay Type
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...
Biomass, leaf number and gas exchange data for Col0 (WT), prr7prr9, and lsf1, compiled from four studies: L&H1-3 and the 'no GA' controls of Gibberellins 1.
Submitter: Andrew Millar
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
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...
Submitter: Ron Henkel
Biological problem addressed: Cell Cycle
Investigation: Hands-on: Model Management in SEEK
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
A boolean network was created using booleannet (after experimenting with Squad and CellNetAnalyzer). This network can be simulated and visualized using additional software components that will be part of the pyMantis CMS that is developed by the Translucent project.
Submitter: Falko Krause
Biological problem addressed: Gene Regulatory Network
Investigation: ENA1 Transcription in Saccharomyces cerevisiae
The main input is the ENA review paper (Function and Regulation of the Saccharomyces cerevisiae ENA Sodium ATPase System, Ruiz&Ariño 2007) and the papers referenced. Another source are the papers linked from the ENA page of SGD http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=ENA1
Submitter: Falko Krause
Biological problem addressed: Gene Expression
Investigation: ENA1 Transcription in Saccharomyces cerevisiae
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
BPG stability analysis
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability