Assays

What is an Assay?

75 Assays visible to you, out of a total of 75

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

SulfoSys, SulfoSys - Biotec

A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-30C

Organisms: No organisms

Models: PGK yeast Fig1a, PGK yeast with/without recycling

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

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

BPG stability analysis

SulfoSys, SulfoSys - Biotec

BPG stability analysis

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: BPG stability

Organisms: No organisms

Models: BPG stability notebook

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 29th Sep 2017 at 13:01, Last updated: 8th Nov 2017 at 14:21

SulfoSys, SulfoSys - Biotec

PGK 70C model

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-70C

Organisms: No organisms

Models: PGK 70C, PGK 70C SBML

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 29th Sep 2017 at 13:08, Last updated: 8th Nov 2017 at 14:21

PGK - GAPDH models

SulfoSys, SulfoSys - Biotec

PGK - GAPDH models

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-GAPDH 30C & 70C

Organisms: No organisms

Models: PGK-GAPDH model Sulfolobus kouril8, PGK-GAPDH model yeast kouril7, PGK-GAPDH models yeast and Sulfolobus Fig. 4

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 29th Sep 2017 at 13:22, 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

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

SulfoSys

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

Submitter: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: PGK Kinetic Model

SOPs: No SOPs

Data files: PGK Kinetic Data, PGK Kinetics Simulation

Snapshots: No snapshots

Created: 1st Aug 2013 at 09:37, Last updated: 8th Nov 2017 at 14:21

Reconstituted Gluconeogenesis System

SulfoSys

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

Submitter: Jacky Snoep

Biological problem addressed: Metabolic Network

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: FBPAase Kinetic Model, GAPDH Kinetic Model, Kinetic Model of Temperature Degradation of Glu..., Model of reconstituted gluconeogenesis system i..., PGK Kinetic Model, TPI Kinetic Model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 1st Aug 2013 at 12:40, Last updated: 8th Nov 2017 at 14:21

Model Validation Gluconeogenesis in S. solfataricus

SulfoSys

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

Submitter: Jacky Snoep

Biological problem addressed: Metabolic Network

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Carbon Loss at High Temperature

Organisms: Sulfolobus solfataricus

Models: Model of reconstituted gluconeogenesis system i...

SOPs: No SOPs

Data files: Experimental Data for Reconstituted Gluconeogen..., Simulation for Reconstituted Gluconeogenic System

Snapshots: No snapshots

Created: 1st Aug 2013 at 12:59, Last updated: 8th Nov 2017 at 14:21

GAPDH Modelling

SulfoSys

Mathematical model for GAPDH kinetics, saturation with BPG, NADPH, NADP, GAP and Pi

Submitter: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: GAPDH Kinetic Model

SOPs: No SOPs

Data files: GAPDH Kinetic Data, GAPDH Kinetics Simulation

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:00, Last updated: 8th Nov 2017 at 14:21

SulfoSys

Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

Submitter: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: TPI Kinetic Model

SOPs: No SOPs

Data files: TPI Kinetic Data, TPI Kinetics Simulation

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:03, Last updated: 8th Nov 2017 at 14:21

FBPAase Modelling

SulfoSys

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Submitter: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: FBPAase Kinetic Model

SOPs: No SOPs

Data files: FBPAase Kinetic data, FBPAase Kinetics Simulation

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:06, Last updated: 8th Nov 2017 at 14:21

Modelling Metabolite Degradation at High Temperature

SulfoSys

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

Submitter: Jacky Snoep

Biological problem addressed: Metabolism

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

Models: Kinetic Model of Temperature Degradation of Glu...

SOPs: No SOPs

Data files: Temperature Degradation Kinetics Simulation, Temperature Degradation of Gluconeogenic Interm...

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:18, Last updated: 8th Nov 2017 at 14:21

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