Assays

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.

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Intra-erythrocytic malaria parasite volumes

Organisms: No organisms

SOPs: No SOPs

Data files: Malaria parasite volumes determined using micro...

Snapshots: No snapshots

Created: 18th Aug 2023 at 07:26, Last updated: 18th Aug 2023 at 07:31

How to use templates for FAIR experimental data representation

Kinetics on the move - Workshop 2016

Here we will use JERM templates with embedded ontologies to describe and annotate example data

Submitter: Olga Krebs

Assay type: Interactomics

Technology type: Technology Type

Investigation: Using SEEK and I-S-A structure to integrate ex...

Study: Experimental study for hands on session

Organisms: No organisms

SOPs: Extraction and quantitative analysis of protein...

Data files: Master template, Transcriptomics Template (ArrayExpress Format)

Snapshots: No snapshots

Created: 27th May 2016 at 11:38, Last updated: 3rd Aug 2023 at 09:45

GLC incubation

Whole body modelling of glucose metabolism in malaria patients

SED-ML: https://jjj.bio.vu.nl/models/experiments/vanniekerk2023_fig4/simulate

Submitter: Dawie van Niekerk

Biological problem addressed: Validation

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Validation of model for malaria-infected erythr...

Organisms: Plasmodium falciparum

Models: GLC incubation timecourses, Kinetic model for incubation (dutoit2)

SOPs: No SOPs

Data files: 5 mM GLC runout data

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:14, Last updated: 29th Jul 2023 at 10:33

Metabolic control analysis

Whole body modelling of glucose metabolism in malaria patients

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Analysis of model for malaria-infected erythroc...

Organisms: Plasmodium falciparum

Models: Kinetic model for steady state (dutoit1), MCA

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 26th Jul 2023 at 11:58, Last updated: 26th Jul 2023 at 12:04

Incubation time for inhibitor treatment

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: Iodoacetic acid (IAA) titrations in cancer cell...

Organisms: No organisms

SOPs: SOP_Cancer cell lines_standard cell culture, SOP_Inhibitor titration intact cells, SOP_Preparation of cell lysates, SOP_Quantification of glycolytic flux (glucose,...

Data files: MDA231_IAA_intact cells_time course

Snapshots: No snapshots

Created: 13th Jul 2023 at 12:59, Last updated: 19th Jul 2023 at 10:34

GAPDH and flux inhibition in MCF7 and MDA231cells

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: Iodoacetic acid (IAA) titrations in cancer cell...

Organisms: Homo sapiens

SOPs: SOP_Cancer cell lines_standard cell culture, SOP_Inhibitor titration intact cells, SOP_Preparation of cell lysates, SOP_Quantification of glycolytic flux (glucose,...

Data files: MCF7_IAA titration_flux_GAPDH_intact cells, MDA231_IAA titration_flux_GAPDH_intact cells

Snapshots: No snapshots

Created: 12th Jul 2023 at 13:18, Last updated: 19th Jul 2023 at 10:19

Target verification/ Specificity of 3BrP in glycolysis

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: 3-Bromopyruvate (3BrP) titrations

Organisms: No organisms

SOPs: SOP_Cancer cell lines_standard cell culture, SOP_Inhibitor titration intact cells, SOP_Preparation of cell lysates

Data files: MDA231_3BrP_intact cells_specificity

Snapshots: No snapshots

Created: 13th Jul 2023 at 13:46, Last updated: 19th Jul 2023 at 10:17

HK, GAPDH and flux inhibition in MDA231 cells

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: 3-Bromopyruvate (3BrP) titrations

Organisms: No organisms

SOPs: SOP_Cancer cell lines_standard cell culture, SOP_Inhibitor titration intact cells, SOP_Preparation of cell lysates, SOP_Quantification of glycolytic flux (glucose,...

Data files: MDA231_3BrP__flux_HK_GAPDH_intact cells

Snapshots: No snapshots

Created: 13th Jul 2023 at 13:25, Last updated: 19th Jul 2023 at 10:15

Traget verification/ Specificity of IAA in glycolysis

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: Iodoacetic acid (IAA) titrations in cancer cell...

Organisms: No organisms

SOPs: No SOPs

Data files: MDA231_IAA_intact cells_specificity

Snapshots: No snapshots

Created: 13th Jul 2023 at 13:08, Last updated: 13th Jul 2023 at 13:55

Predicting urinary acylcarnitines under metabolic decompensation.

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

(Show All)

Prediction of patient urinary acylcarnitine under metabolic decompensation. Generates Fig. 3, Table 1, and Table S2 in the associated publication.

Download and unzip "Model_notebooks.rar" and run "7, Fig3+4+S1+S3-ACADDs-[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

Organisms: No organisms

Models: Model notebooks, odendaal1

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 7th Mar 2023 at 11:08, Last updated: 13th Jun 2023 at 14:53

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