Assays

What is an Assay?

40 Assays visible to you, out of a total of 40

Inhibition of glycolytic flux

Whole body modelling of glucose metabolism in malaria patients

Inhibition of lactate flux glycolytic inhibitors

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: Glycolytic target analysis in malaria infected ..., Inhibition of glycolytic flux by glucose transp..., Kinetic model for steady state (dutoit1), Validation of lactate flux inhibition by glucos...

SOPs: No SOPs

Data files: Glycolytic flux inhibition data (erythrocytes), Lactate flux inhibition data

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:26, Last updated: 18th Aug 2023 at 08:21

Flux vs external glucose

Whole body modelling of glucose metabolism in malaria patients

No description specified

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: Flux vs glucose, Kinetic model for infected red blood cell cultu...

SOPs: No SOPs

Data files: Flux vs glucose

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:21, Last updated: 18th Aug 2023 at 07:59

Steady-state

Whole body modelling of glucose metabolism in malaria patients

No description specified

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: Kinetic model for steady state (dutoit1), Steady state (trophozoite stage)

SOPs: No SOPs

Data files: Stage specific fluxes

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:18, Last updated: 18th Aug 2023 at 07:45

Malaria parasite volume determinations

Whole body modelling of glucose metabolism in malaria patients

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

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

Stage specific fluxes

Whole body modelling of glucose metabolism in malaria patients

No description specified

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: Kinetic model for steady state (dutoit1), Stage specific fluxes

SOPs: No SOPs

Data files: Stage specific fluxes

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:23, Last updated: 25th Apr 2023 at 16:41

Flux vs parasitaemia

Whole body modelling of glucose metabolism in malaria patients

No description specified

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: Flux vs parasitaemia, Kinetic model for infected red blood cell cultu...

SOPs: No SOPs

Data files: Flux vs parasitaemia

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:20, Last updated: 25th Apr 2023 at 11:52

gustavsson1-4 models

Yeast glycolytic oscillations

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Sustained glycolytic oscillations in individual...

Organisms: No organisms

Models: gustavsson1-4 models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:38

gustavsson5 model

Yeast glycolytic oscillations

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Allosteric regulation of phosphofructokinase co...

Organisms: No organisms

Models: gustavsson5 model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:18

Source data for Figure 2: Experimental time-resolved quantitative immunoblot data

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Adlung et al (2017) Molecular Systems Biology

Study: Figure 2: Model calibration with time-resolved ...

Organisms: No organisms

SOPs: No SOPs

Data files: Source data for Figure 2B, Source data for Figure 2C, Source data for Figure 2D, Source data for Figure 2E, Source data for Figure 2F BaF3, Source data for Figure 2F mCFU-E, Source data for Figure 2G BaF3, Source data for Figure 2G mCFU-E

Snapshots: No snapshots

Created: 11th Jan 2017 at 10:38, Last updated: 8th Nov 2017 at 14:21

Culturing and synchronisation of P. falciparum

Whole body modelling of glucose metabolism in malaria patients

No description specified

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 15th Aug 2014 at 13:01, Last updated: 8th Nov 2017 at 14:21

Trophozoite Isolation and Lysate Preparation

Whole body modelling of glucose metabolism in malaria patients

Assay for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 15th Aug 2014 at 13:02, Last updated: 8th Nov 2017 at 14:21

Source data for Figure 3A: Experimental quantitative immunoblotting data.

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Bachmann et al (2011) Molecular Systems Biology...

Study: Figure 3A: Model calibration with experimental ...

Organisms: No organisms

SOPs: No SOPs

Data files: Source data for Figure 3A: Experimental quantit...

Snapshots: No snapshots

Created: 3rd Mar 2016 at 10:01, Last updated: 8th Nov 2017 at 14:21

Kinetic model of antibiotic-mediated inhibition of ribosomes

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Srimani et al (2017) Molecular Systems Biology

Study: Figure 2C Panel ii: After the removal of the ex...

Organisms: No organisms

Models: Kinetic model of antibiotic-mediated inhibition...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 26th Sep 2017 at 09:59, Last updated: 8th Nov 2017 at 14:21

Mathematical models of the Epo-induced AKT, ERK and S6 activation.

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Adlung et al (2017) Molecular Systems Biology

Study: Figure 2: Model calibration with time-resolved ...

Organisms: No organisms

Models: BaF3 model, mCFU-E model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 12th Jan 2017 at 08:19, Last updated: 8th Nov 2017 at 14:21

Inhibition of glucose transport

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 tro...

Study: Model analysis

Organisms: Plasmodium falciparum

Models: GLCtr kinetic model incorporating inhibition

SOPs: No SOPs

Data files: GLCtr inhibition kinetic data

Snapshots: No snapshots

Created: 2nd Jul 2015 at 10:24, Last updated: 8th Nov 2017 at 14:21

Inhibition of lactate flux

Whole body modelling of glucose metabolism in malaria patients

Inhibition of lactate flux due to glucose transport inhibitor

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model analysis

Organisms: Plasmodium falciparum

Models: Kinetic model for steady state (penkler1), Kinetic model incorporating glucose transport i..., Validation of lactate flux inhibition by glucos...

SOPs: No SOPs

Data files: Lactate flux inhibition data

Snapshots: No snapshots

Created: 2nd Jul 2015 at 10:33, Last updated: 8th Nov 2017 at 14:21

Supply-demand 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 tro...

Study: Model analysis

Organisms: Plasmodium falciparum

Models: Kinetic model for steady state (penkler1), Supply demand analysis on penkler1 model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jul 2015 at 10:28, Last updated: 8th Nov 2017 at 14:21

Model for JAK2/STAT5 signaling

Molecular Systems Biology

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Bachmann et al (2011) Molecular Systems Biology...

Study: Figure 3A: Model calibration with experimental ...

Organisms: No organisms

Models: JAK2/STAT5 model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 3rd Mar 2016 at 10:04, Last updated: 8th Nov 2017 at 14:21

Model nuclear receptor (NR) signaling

Molecular Systems Biology

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Kolodkin et al (2010) Molecular Systems Biology...

Study: Figure 2B: Transcriptional response to a sudde...

Organisms: No organisms

Models: NR model 1, NR model 2, NR model 3, NR model 4, NR model 5, NR model 6

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 17th May 2016 at 12:18, Last updated: 8th Nov 2017 at 14:21

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of HK.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: HK Kinetic model

SOPs: HK Kinetic characterisation

Data files: HK Kinetic data

Snapshots: Snapshot 1

Created: 8th Aug 2014 at 13:30, Last updated: 8th Nov 2017 at 14:21

PGI

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of PGI.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: PGI Kinetic model

SOPs: PGI Kinetic characterisation

Data files: PGI Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:27, Last updated: 8th Nov 2017 at 14:21

PFK

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of PFK.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: PFK Kinetic model

SOPs: PFK Kinetic characterisation

Data files: PFK Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:29, Last updated: 8th Nov 2017 at 14:21

ALD

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of ALD.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: ALD Kinetic model

SOPs: ALD Kinetic characterisation

Data files: ALD Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:30, Last updated: 8th Nov 2017 at 14:21

TPI

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of TPI.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: TPI Kinetic model

SOPs: TPI Kinetic characterisation

Data files: TPI Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:31, Last updated: 8th Nov 2017 at 14:21

G3PDH

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of G3PDH.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: G3PDH Kinetic model

SOPs: G3PDH Kinetic characterisation

Data files: G3PDH Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:32, Last updated: 8th Nov 2017 at 14:21

GAPDH

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of GAPDH.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: GAPDH Kinetic model

SOPs: GAPDH Kinetic characterisation

Data files: GAPDH Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:33, Last updated: 8th Nov 2017 at 14:21

PGK

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of PGK.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: PGK Kinetic model

SOPs: PGK Kinetic characterisation

Data files: PGK Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:34, Last updated: 8th Nov 2017 at 14:21

PGM

Whole body modelling of glucose metabolism in malaria patients

Kinetic characterisation en mathematical modelling of PGM.

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Organisms: No organisms

Models: PGM Kinetic model

SOPs: PGM Kinetic characterisation

Data files: PGM Kinetic data

Snapshots: No snapshots

Created: 11th Aug 2014 at 07:35, Last updated: 8th Nov 2017 at 14:21

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