Virtual Liver SEEK

4 items tagged with 'SBML qual'.

Publications (4)

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

Authors: Clemens Wrzodek, Andreas Dräger, Andreas Zell

PubMed ID: 21700675

Date Published: 25th Jun 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase Steatosis

Journal: Bioinformatics

Citation: Bioinformatics 27(16): 2314-5

Scales: Cell and Intercellular

Abstract (Expand)

SUMMARY: The KEGG PATHWAY database provides a widely used service for metabolic and non-metabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and ...

Created: 30th Jun 2011 at 08:35 Last updated: 24th Oct 2013 at 16:18

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Authors: Claudine Chaouiya, Duncan Berenguier, Sarah M Keating, Aurelien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomá¿ Helikar

DOI: 10.1186/1752-0509-7-135

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 135

Scales: Cell and Intercellular

Abstract (Expand)

Background Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is ...

Created: 10th Dec 2013 at 18:07 Last updated: 10th Dec 2013 at 18:09

Path2Models: large-scale generation of computational models from biochemical pathway maps

Authors: Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère

DOI: 10.1186/1752-0509-7-116

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 116

Scales: Cell and Intercellular

Abstract (Expand)

Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de ...

Created: 4th Nov 2013 at 16:48 Last updated: 4th Nov 2013 at 16:54

Precise generation of systems biology models from KEGG pathways

Authors: Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell

DOI: 10.1186/1752-0509-7-15

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 15

Scales: Cell and Intercellular

Abstract (Expand)

Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG ...

Created: 23rd Feb 2013 at 23:19 Last updated: 24th Oct 2013 at 16:15