Assays

What is an Assay?
978 Assays visible to you, out of a total of 1941

This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for ...

This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. Instructions to run the Photoperiodism Model in Simile 1.       Save all the files into the same folder. 2.       Copy and paste the attached ‘lightfunction.pl’ file in the following folder:            Program File > Simile6.0 (or other software version)> Functions 3.       Download the ...

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

Application of the LoRAS oversampling approach on single-cell/single-nuclei data to annotate/identify specific cell populations in new data based on previously, manually curated data.

For scRNA-Seq, iSABs were dissociated using the Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) before library preparation was performed using the 10xGenomics system with subsequent sequencing on the HighSeq4000 (Illumina). The mouse-SAN scRNA-Seq protocol is described in Goodyer et al. Preprocessing of raw sequencing data from iSABs relied on tools of the Cell Ranger Software (v.6.1.0) as was the procedure in Goodyer et al. Downstream analyses were conducted similar for both ...

Submitter: Anne-Marie Galow

Biological problem addressed: Gene Expression

Investigation: 1 hidden item

Study: Quality control in scRNA‑Seq can discriminate p...

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Specific activity of Gre2p measured by following the change in absorbance of NADPH at 340 nm for the conversion of nitrononane-2,8-dione (NDK) using different enzyme concentrations.

effects of 1% increase in each parameter, more detailed analysis of water content

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Model simulation of cortisone or 11KA4 metabolism in human subcutaneous and omental adipose tissue, and the effect of AZD4017 inhibition of HSD11B1.

This is the simulation part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

Submitter: Gudrun Gygli

Assay type: Molecular Dynamics

Technology type: All-Atom

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Scripts for running network simulations

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Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558

Originally submitted to PLaSMo on 2011-08-12 15:34:00

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Specific activity of Gre2p measured by following the change in absorbance of NADPH at 340 nm for the conversion of nitrononane-2,8-dione (NDK).

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The membrane potential of cells grown overnight in a certain concentration of KCl will be determined, to reveal a relation between external KCl and a possibly stable membrane potential. See also "2D-Gel Electrophoresis " Assay for further details.

The pH of cells grown overnight in a certain concentration of KCl will be determined, to reveal a functional relationship between external KCl and a stable pH. See also "2D-Gel Electrophoresis" Assay for further details.

The potassium content of cells grown overnight in a certain amount (0.1, 0.2, 0.5, 1, 5, 20, 50, 200 mM) of KCl will be determined. Additionally the potassium content of cells grown overnight in high potassium and shifted to the amounts of potassium used in the former experiment. After growing overnight again in the lower potassium, the cells should contain finally a comparable potassium concentration than the cells grown in the respecting KCl in the first experiment.

The volume of cells grown overnight in a certain concentration of KCl will be determined, to reveal a relation between the osmotic effects of external KCl and the cell volume. See also 1.4.1. for further details.

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Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

The statistical analysis was performed in a jupyter notebook. This notebook contains the commands for all performed analyses (Statistical_analysis_of_FAIR_citations.ipynb)

The Bayesian Estimation Superseeds the t Test (BEST) method of Kruschke 2013 was used for the Bayesian significance testing. The method was implemented in a python class together with visualization and distributional analysis methods (BEST_method_python_Kruschke2012.py). Also the bayesian multiple comparison analysis can be ...

Submitter: Sebastian Höpfl

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: Bayesian hypothesis testing reveals that reprod...

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Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model validation

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Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D = 0.1 h-1 on minimal medium

experimentally measured extracellular fluxes in yeast Saccharomyces cerevisiae in anaerobic glucose limited chemostat (D=0.1 h-1) on minimal medium

The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.

Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.

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Submitter: Mohamed Albadry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Periportal steatosis in mice affects distinct p...

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.

The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This ...

Measurements of acetone, butanol, acetate, butyrate and ethanol taken during dynamic shift (pH 5.8, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5) and at steady state (pH 5.7, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5).

The model is applied to spring wheat, with ample supply of nutrients and water, also without pests, diseases and weeds. Radiation and temperature, being the most important environmental factors, and crop characteristics determine growth and development. Crop growth and development are simulated based on underlying chemical, physiological and physical processes. Dry matter accumulation is calculated from daily crop CO2 assimilation based on leaf CO2 assimilation and taking into account the respiration ...

Supplemental files for the publication

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Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model analysis

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