Assays

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

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

Based on odendaal1, a control model is made and compared to model deficient for short-chain acyl-CoA dehydrogenase (SCADD, 0%), medium-chain acyl-CoA dehydrogenase (MCADD, 0%), and very long-chain acyl-CoA dehydrogenase (VLCADD, 10%). With and withou metabolite partitioning, and with a fixed mitohondrial free CoASH. Generates Figures 3, 4, S1, S2, and S3 in the related paper.

Download "Model_notebooks.rar", unzip, and run: "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" and "14, ...

Submitter: Christoff Odendaal

Biological problem addressed: Model Analysis Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model analysis

No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified
No description specified

Submitter: Yi Chen

Biological problem addressed: Gene Expression

Investigation: FAIR Functional Enrichment: Assessing and Model...

Study: FAIR Functional Enrichment

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.

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.

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

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.

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.

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...

No description specified

Submitter: Vincent Wagner

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: SiCaSMA: An alternative stochastic description ...

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.

No description specified
No description specified

Submitter: Mohamed Albadry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

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

No description specified

Submitter: Mohamed Albadry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

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

No description specified

Submitter: Mohamed Albadry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

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

Powered by
(v.1.14.2)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH