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Created: 20th Feb 2013 at 15:40
Last updated: 28th Feb 2013 at 14:30
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Projects: SysMO DB, HUMET Startup, FAIRDOM
Institutions: University of Leiden

Expertise: Data Management, Bioinformatics, Biochemistry
Tools: semantic web, Taverna, Ontologies, Workflows, Web services, Databases, Transcriptomics, Data Management
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Not specified
Investigating oscillations at the level of yeast populations and individual cells
Snapshots: No snapshots
Studies: Detailed kinetics of yeast glycolytic oscillation, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations, Modelling sustained glycolytic oscillations in individual isolated yeast...
Concentration of glycolytic intermediates over time
Contributor: Katy Wolstencroft
Assay type: Discontinuous Enzymatic
Technology type: Enzymatic Activity Measurements
Snapshots: No snapshots
Investigation: Yeast Glycolytic Oscillations
Study: Detailed kinetics of yeast glycolytic oscillation
Organisms: Saccharomyces cerevisiae (batch)
SOPs: No SOPs
Data files: Das (1991) NADH and ATP concentrations determin..., Richard (1996) Concentrations of oscillating gl...
Contributor: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Yeast Glycolytic Oscillations
Study: Detailed kinetics of yeast glycolytic oscillation
Organisms: Saccharomyces cerevisiae
Models: Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci...
SOPs: No SOPs
Data files: Das (1991) NADH and ATP concentrations determin..., Das (1991) Time varying concentrations for meta..., Richard (1996) Concentrations of oscillating gl... and 7 hidden items
Creators: Franco Du Preez, Jacky Snoep
Contributor: Franco Du Preez
Investigations: Yeast Glycolytic Oscillations
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez1) is the basis kinetic model derived from that published by Teusink et al., 2000 (PMID: 10951190).
Creators: Franco Du Preez, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez2) is an oscillating version of the basis kinetic model (dupreez1) derived from that published by Teusink et al., 2000 (PMID: 10951190).
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez3) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996 (PMID: 8813760).
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez4) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996a (PMID: 8813760) as well as the rapid synchronization following the mixing of two yeast cultures that oscillate 180 degrees out of
...
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez5) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the amplitude bifurcation of oscillating yeast cultures in a CSTR setup reported by Hynne et al., 2001 (PMID: 11744196).
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez6) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in cell free extracts of oscillating yeast cultures reported by Das and Busse, 1991 (PMCID: 1260073).
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez7) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the fluorescence signal of NADH in oscillating yeast cultures reported by Nielsen et al., 1998 (PMID: 17029704).
Creators: Franco Du Preez, Jacky Snoep, David D van Niekerk
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Yeast Glycolytic Oscillations
Studies: Detailed kinetics of yeast glycolytic oscillation
Modelling analyses: Detailed kinetic model of yeast glycolytic osci...
Abstract (Expand)
Authors: Franco Du Preez, Jacky Snoep, van Niekerk David D,Kooi Bob,Rohwer Johann M
Date Published: 21st Jun 2012
Journal: The FEBS journal
PubMed ID: 22712534
Citation:
Abstract (Expand)
Authors: Franco Du Preez, Jacky Snoep, van Niekerk David D
Date Published: 13th Jun 2012
Journal: The FEBS journal
PubMed ID: 22686585
Citation: