The SEEK DEMO

8 items tagged with 'SBML'.

Projects: STREAM

Disciplines: Not specified

Expertise: Comparative Genomics, Data integration, Database and data warehouse design, High-throughput sequence analysis, Phylogenetics, Systems Biology, Bioinformatics, Software Engineering

Tools: BioMart, HTML, XML, EnsEMBL, R, Perl, SBML, Databases

Systems Biologist specialising in data integration, high-throughput sequence analysis and phylogenetics.

Peter Götz

Projects: COSMIC

Institutions: University of Stuttgart

Disciplines: Not specified

Roles: Sysmo-DB Pal

Expertise: Data integration, Nonlinear Dynamics, Optimal experimental design, Dynamic optimization., bioreactor models, rapid sampling experiments, parameter estimation, dynamics of biological networks, coupling metabolome and environome, Mathematical modelling, Data Management

Tools: Dynamic modelling, evaluation of process dynamics, continuous cultivation, Material balance based modeling, stimulus response experiments, Matlab, Fermentation, SBML

Process engineer, modeling biological systems since 1985.

Sebastian Henkel

Projects: SUMO

Institutions: University of Stuttgart

Disciplines: Modeller

Roles: Member, Sysmo-DB Pal

Expertise: Systems Biology, parameter estimation, Mathematical modelling, Data Management

Tools: Matlab, Mathematica, SBML, ODE

PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO.

Falko Krause

Projects: TRANSLUCENT

Institutions: Humboldt-Universität zu Berlin

Disciplines: Not specified

Roles: Not specified

Expertise: Not specified

Tools: semanticSBML, PHP, MIRIAM, SQL, linux, Python, SBML, Bioinformatics, Data Management

Mark Musters

Projects: SysMO-LAB

Institutions: University of Wageningen

Disciplines: Not specified

Roles: Sysmo-DB Pal

Expertise: dynamics of biological networks, Reactor models, Mathematical modelling, Bioinformatics

Tools: SQL, Material balance based modeling, Matlab, Mathematica, JWS Online, Copasi, Algebraic equations, ODE, Linear equations, Partial differential equations, Metabolomics, Model organisms, SBML, Cell biology, Computational and theoretical biology, Molecular Biology

No description specified

Stefan Gayer

Projects: KOSMOBAC

Institutions: Max-Planck-Institute Magdeburg

Disciplines: Not specified

Roles: Sysmo-DB Pal

Expertise: dynamics and control of biological networks, parameter estimation, Mathematical modelling

Tools: DIVA, ProMOT, differential algebraic equations, Matlab, ODE, SBML

No description specified

Teusink

SysMO DB

This model is for a paper that examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In non-growing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under
...

Creator: Stuart Owen

Contributor: Stuart Owen

Model type: Not specified

Model format: SBML

Organism: Saccharomyces cerevisiae

Environment: Not specified

Scales: Genomics (param:gluc2 unit:mg) and Aveoli (param:width unit:mm)

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Created: 9th Jun 2009 at 16:46, Last updated: 21st Apr 2015 at 12:21

Annotation and merging of SBML models with semanticSBML

TRANSLUCENT

Abstract (Expand)

SUMMARY: Systems Biology Markup Language (SBML) is the leading exchange format for mathematical models in Systems Biology. Semantic annotations link model elements with external knowledge via unique ...

Authors: Falko Krause, Uhlendorf Jannis,Lubitz Timo,Schulz Marvin,Klipp Edda,Liebermeister Wolfram

Date Published: 17th Nov 2009

Journal: Bioinformatics

PubMed ID: 19933161

Citation:

Scales: Not specified

Created: 5th Jul 2010 at 16:13