Assays

What is an Assay?
978 Assays visible to you, out of a total of 1941
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To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.

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To obtain each of the figure 4A - 4D please download "Main Figure 4 Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.

Determinations of parasite volumes in a well-synchronised, infected culture treated with a cytosolic stain, using fluorescence microscopy. Diameters used to calculate parasite volume, assuming a spherical parasite cell.

Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.

Test by Martin for simileXML

Originally submitted to PLaSMo on 2012-03-08 11:39:23

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Beaton, Martin

Study: Martin test - PLM_65

Test by Martin for simileXML

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Version 2, the product of many seconds of research..



Originally submitted to PLaSMo on 2012-03-08 11:39:23

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Beaton, Martin

Study: Martin test - PLM_65

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L. lactis, E. faecalis and S. pyogenes are referred to as LAB because of the fact that in the presence of glucose lactate is produced as the main fermentation product . This metabolic pathway is relatively inefficient, since only 2 ATP are generated from one glucose molecule. All three LAB possess the genetic make up for mixed acid fermentation, a more effective way of fermentation generating 3 ATP per molecule of glucose. All three genomes reveal (at least) two genes encoding a lactate dehydrogenase ...

Creation of personalised models of control, symptomatic MCADD, asymptomatic MCADD, and early diagnosis MCADD individuals using fibroblast proteomics to adjust model Vmaxes. Generates Fig. 7 and S7.

Download and unzip "Model_notebooks.rar" and run "13, Fig7-personalised-models-[needs-(1-and-12)]-20221109.nb" after running "1, generate-model-20221109.nb" and "12, Fig7-S7-preprocessing-[needs-(1)-]-20221109.nb".

Submitter: Christoff Odendaal

Biological problem addressed: Model Analysis Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model analysis

Incrementally increase the activity of some target rescue enzymes from 20% of default expression to 200% of default expression in a control and MCADD model to see if flux and CoASH concentration are rescued. Generates Fig. 6, S5, and S6.

Download "Model_notebooks.rar", unzip, and run "11, Fig6+S5-rescues-[needs-(1-and-10)]-20221109.nb", "10, Fig6B-inset-rescues-(low-acetylCoA)-[needs-(1)]-20221109.nb", and "16, FigS6-rescues-20221109-fixed-[needs-(1)]-CoASH.nb" after running "1, generate-model-20221109.nb" ...

Submitter: Christoff Odendaal

Biological problem addressed: Model Analysis Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model analysis

This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...

This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...

This .csv file shows the numbers of different cytochrome molecules per cell from steady-state continuously-grown cultures at various aerobiosis levels (0%, 31%, 56%, 85% and 115% AAU).

To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.

To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.

Calculation of control and response coefficients. Generates Fig. 5, Fig. S4, and Table S2 in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "8, Fig5-control-coefficients-[needs-(1)]-20221109.nb", "9, TableS2-response-coefficients-[needs-(1)]-20230302.nb", and "15, FigS4-control-coefficients-low-AcetylCoA-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Submitter: Christoff Odendaal

Biological problem addressed: Model Analysis Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model analysis

No description specified

Metabolic control analysis: Local control coefficients for 40 independent samples based on 100x sampling from the measurement distribution Global control analysis based on 100.000 Latin Hypercube sampling from the parameter search range (0.01-100 for Km values and 0.001-1000 for Vmax values)

Genome scale metabolic model of Sulfolobus solfataricus specific scenario: modelling of L-fucose degradation pathways

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Concentration of glycolytic intermediates over time

Metabolite profiling on T. brucei exposed to methylene blue has been carried out using LC-MS to investigate metabolic changes caused by oxidative stress

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Measurement of intra- and extra-cellular metabolome.

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NB! The files here are the old version for the files in Lipidomics (Experimental Assay)

Lipidomic analysis by LC-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.

There are two separate data files of lipid analysis in muscle and liver samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.

We have also performed a "normalization ...

Global metabolomics screening of 36 liver samples from Atlantic cod exposed to chlorpyrifos-methyl for 30 days.

Submitter: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: In vivo Nord 1: Chlorpyrifos-methyl

Measurements of external metabolites based on growth curve data. Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate

Metabolomics time series measurements for internal metabolites for 6h, 24h and 48h for multiple experiments. Largely based on MAss spectrometry, bioluminescence kits to measure NAD, NADH at 24h, other time points are infered from relative measurements times the absolute measurements at 24h.

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.

Curation guidelines for molecular interaction causal statements

RNAi Screen of 100 candidate genes predicted to be involved in mitotic chromosome condensation. MIHCSME template example for IDR0002 dataset.

MIHCSME template example for IDR0022 dataset. Primary and validation RNAi screen using smartpool and single siRNAs to identify cell migratory regulators in Hs578T and MDA-MB-231 triple-negative breast cancer cells.

Compound screen on 13 HepG2 -GFP reporter lines, to measure GFP protein induction, and cell death induction. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.

Compound screen on HepG2 CHOP-GFP reporter, to measure CHOP-GFP protein induction upon treatment with compounds. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.

Validation: Validated against the original running in Excel. Each calculation in the model was individually validated as well. Comments on numerical integration: Euler integration with time steps of 1. In Simile the "time units" were set to "day" and execution was for 364 days as the simulation starts at time 0 (not time 1 as in the Excel model). Comments on running Simile model: Users must specify the temperature controlled growing season themselves. To do this use the following steps which take ...

Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods

Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods

Model simulations for 24h incubations with different ratios of HSD11B1 andd AKR1C3 transfected HEK293 cells are given in Mathematica notebook format.

A mathematica notebook that simulates the combined effect of HSD11B1/AKR1C3 ratio variation and HSD11B1 inhibition.

Lumped kinetic model of L. lactis glycolysis, formulated with ordinary differential equations. Simulations are in line with experimental data

HSD11B1 was inhibitied by CBX and the effect of the inhibition on cortisone and 11KA4 conversion was simulated. The model was coded in Mathematica and the f=manuscript figures 3 A,B,C,D,E anbd F are presented in the notebook.

Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate

Model files accompanying Seaton et al., Molecular Systems Biology, 2015 Abstract: Clock?regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best?understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN?BINDING, KELCH REPEAT, F?BOX 1 (FKF1) transcription. ...

Modelling the degradation of BPG, GAP and DHAP at high temperature

Based on a kinetic model a description of the potassium current is achieved. Its properties with respect to changes in membrane potential and potassium concentrations are derived.

The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length

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This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . Originally submitted to PLaSMo on 2012-03-29 10:24:44

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The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.

This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression. 3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the ...

Alignments of various alpha-tubulin and beta-tubulin sequences from dinitroaniline-sensitive and dinitroaniline-resistant species. Sequences were retrieved from UniProt with the identifiers listed below and subjected to a multiple sequence alignment using ClustalOmega (ebi.ac.uk/Tools/msa/clustalo/; ClustalOmega webserver, last accessed 16-02-23):

alpha-tubulin:

  • [dinitroaniline sensitive] T. cruzi - Q27352; T. brucei brucei - Q4GYY5; L. infantum - ...
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