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

Metabolic control analysis

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

(Show All)

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

Organisms: No organisms

Models: Model notebooks, odendaal1

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

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

MCADD patient personalised modelling

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

(Show All)

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

Organisms: No organisms

Models: Model notebooks, odendaal1

SOPs: No SOPs

Data files: Fibroblasts proteomics

Snapshots: No snapshots

Created: 7th Mar 2023 at 13:57, Last updated: 12th Jun 2023 at 13:33

HepG2 oxygen consumption

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

(Show All)

Validation of model's ability to predict oxygen consumption flux as measured usign permeabilised cells in an Oroboros Oxygraph. Generates Fig. 2A in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "4, Fig2A-Oroboros-simulation-data-[needs-(1-2-and-3)]-20221109.nb" after running "1, generate-model-20221109.nb"

Submitter: Christoff Odendaal

Biological problem addressed: Validation

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model validation

Organisms: Homo sapiens

Models: Model notebooks, odendaal2

SOPs: No SOPs

Data files: HepG2 protein concentration for O2 consumption ..., Oxygen concentration and consumption flux in pe...

Snapshots: No snapshots

Created: 23rd Feb 2023 at 14:41, Last updated: 12th Jun 2023 at 13:30

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