The FAIRDOMHub

13 items tagged with 'Kinetic modelling'.

Projects: Not specified

Institutions: Not specified

Disciplines: Not specified

Roles: Not specified

Expertise: genome-scale modeling, Biochemistry, Software Engineering, Metabolic Control Analaysis, constraint-based modelling, SBML, standards, Kinetic modelling, Python

Tools: SBML, SED-ML, Web services, metabolic network visualization, libSBML, FBA, kinetic modeling, F-A-M-E, Python, PySCeS, CBMPy, JWS Online

Biochemist currently keeping busy as: Research Data Manager (Vrije Universiteit Amsterdam), Software Engineer (Heidelberg University) and member of the SBML Development Team (Caltech).

Mary-Ann Blätke

Projects: Not specified

Institutions: Not specified

Disciplines: Modeller, Bioinformatician

Roles: Not specified

Expertise: Metabolic Engineering, Kinetic modelling, dynamics and control of biological networks, Bioinformatics, Databases, Mathematical modelling, Molecular Biology, Systems Biology

Tools: SBML, Python, Petri Nets, Snoopy, Marcie, Charlie, Matlab, Jupyter, FBA, MySQL, HTML, Javascript, PHP, CSS

No description specified

Egils Stalidzans

Projects: LEANPROT, FAIRDOM user meeting

Institutions: Latvia University of Agriculture, Institute of Microbiology and Biotechnology, University of Latvia

Disciplines: Modeller, Admin

Roles: Vice Coordinator

Expertise: Kinetic modelling, parameter estimation, optimization

Tools: Copasi, COBRA toolbox

No description specified

Matthias König

Projects: Kinetics on the move - Workshop 2016, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), FAIRDOM user meeting, COMBINE Multicellular Modelling

Institutions: Charité University Medicine Berlin, Humboldt-Universität zu Berlin, Humboldt University Berlin

Disciplines: Modeller, Bioinformatician

Roles: Project Coordinator

Expertise: metabolic networks, Kinetic modelling, Liver, Metabolic Models, Computational modelling, computational biology

Tools: SBML, SED-ML, ODE, roadrunner, tellurium, Cytoscape

We are investigating liver metabolism and function with the help of computational models and methods.
Read more about the LiSyM junior group at: www.livermetabolism.com

Junior Group Leader
Dr. Matthias König

Institute for Theoretical Biology
Humboldt-University Berlin
Invalidenstraße 43, 10117 Berlin, Germany
phone +49 30 2093-8450
konigmatt@googlemail.com

The liver is the central metabolic organ of our body playing a crucial role in the clearance of drugs, xenobiotics and numerous metabolites
...

Ali Salehzadeh-Yazdi

Projects: SYSTERACT, Kinetics on the move - Workshop 2016

Institutions: University of Rostock

Disciplines: Modeller, Bioinformatician

Roles: Postdoc

Expertise: metabolic systems biology, Kinetic modelling, metabolic networks

Tools: Cytoscape, Copasi, COBRA toolbox, R

No description specified

Eduard Kerkhoven

Projects: SilicoTryp, SYSTERACT

Institutions: University of Glasgow, Chalmers University of Technology

Disciplines: Modeller, Experimentalist

Roles: Member

Expertise: genome-scale modeling, Kinetic modelling, metabolism, Data integration, Metabolomics, Metabolic Engineering, Transcriptomics, Microbiology

Tools: COBRA toolbox, Copasi, RNAseq, Bioreactor experiments, Metabolomics, Dynamic modelling, R, Matlab

No description specified

Natalie Stanford

Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting

Institutions: School of Computer Science, University of Manchester, Manchester Centre for Integrative Systems Biology, University of Manchester

Disciplines: Modeller

Roles: Member, Postdoc

Expertise: Data Management, Stoichiometric modelling, Kinetic modelling, Systems Biology, Metabolic Engineering, metabolic networks

Tools: COBRA toolbox, Python, Copasi, Matlab

Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.

Detailed kinetic model of yeast glycolytic oscillation - I

SysMO DB

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

Organism: Saccharomyces cerevisiae

Environment: JWS Online

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Created: 16th Jul 2012 at 13:33, Last updated: 23rd Jul 2012 at 01:28

SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten

LiSyM Core Infrastructure and Management (LiSyM-PD), Kinetics on the move - Workshop 2016

(Show All)

Abstract:

Not specified

Authors: Wolfgang Müller, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig, Bittkowski Meik

Date Published: 1st Mar 2017

Journal: Datenbank Spektrum

DOI: 10.1007/s13222-016-0243-4

Citation: Datenbank Spektrum 17(1) : 21

Created: 6th Apr 2017 at 11:48, Last updated: 6th Apr 2017 at 11:49

From steady-state to synchronized yeast glycolytic oscillations I: model construction

SysMO DB

Abstract (Expand)

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original ...

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:

Created: 16th Jul 2012 at 11:35

From steady-state to synchronized yeast glycolytic oscillations II: model validation

SysMO DB

Abstract (Expand)

In an accompanying paper [du Preez et al., (2012) FEBS J doi: 10.1111/j.1742-4658.2012.08665.x], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. ...

Authors: Franco Du Preez, Jacky Snoep, van Niekerk David D

Date Published: 13th Jun 2012

Journal: The FEBS journal

PubMed ID: 22686585

Citation:

Created: 16th Jul 2012 at 11:32

Sustained glycolytic oscillations in individual isolated yeast cells

SysMO DB

Abstract (Expand)

Yeast glycolytic oscillations have been studied since the 1950s in cell-free extracts and intact cells. For intact cells, sustained oscillations have so far only been observed at the population level, ...

Authors: Franco Du Preez, Jacky Snoep, Gustavsson Anna-Karin,van Niekerk David D,Adiels Caroline B,Goksör Mattias

Date Published: 23rd May 2012

Journal: The FEBS journal

PubMed ID: 22607453

Citation:

Created: 16th Jul 2012 at 11:28

Graph based storage and retrieval of computational models

SysMO DB

Presented by Ron Henkel at SySMO PALs meeting 29-30 November 2012 in Heidelberg

Creator: Ron Henkel

Contributor: Olga Krebs

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Created: 6th Dec 2012 at 14:13