Virtual Liver SEEK

6 items tagged with 'modelling'.

Publications (5)

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Authors: Michael Hucka, David P. Nickerson, Gary D. Bader, Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le NovÃ¨re

DOI: 10.3389/fbioe.2015.00019

Date Published: 24th Feb 2015

Projects: F1: The data management system, Virtual Liver

Journal: Front. Bioeng. Biotechnol.

Citation: Front. Bioeng. Biotechnol. 3

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s ...

Created: 25th Feb 2015 at 12:58 Last updated: 25th Feb 2015 at 13:01

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

DOI: 10.4056/sigs.5279417

Date Published: 15th Mar 2014

Projects: F1: The data management system

Journal: Stand. Genomic Sci.

Citation: Stand. Genomic Sci. 9(3) : 1285

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report ...

Created: 3rd Feb 2015 at 11:07 Last updated: 3rd Feb 2015 at 11:12

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Authors: Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

PubMed ID: 25494900

Date Published: 14th Dec 2014

Projects: F1: The data management system

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 15(1): 369

Scales: Not specified

Abstract (Expand)

BackgroundWith the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more ...

Created: 9th Jan 2015 at 15:06

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

CySBML: a Cytoscape plugin for SBML

Authors: Matthias König, Andreas Dräger, Hermann-Georg Holzhütter

PubMed ID: 22772946

Date Published: 10th Jul 2012

Projects: A1: Cellular metabolism, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, F: Data management

Journal: Bioinformatics (Oxford, England)

Citation: Bioinformatics 28(18): 2402-3

Scales: Not specified

Abstract (Expand)

SUMMARY: CySBML is a plugin designed to work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts ...

Created: 12th Jul 2012 at 08:37 Last updated: 24th Oct 2013 at 16:16

Presentations (1)

Presentation: From Hepatocytes to Whole Liver Function: A Multi-scale Model of Human Galactose Metabolism (VLN Retreat 2013)

Uploader: Matthias König

Contributor: Hermann-Georg Holzhütter, Matthias König

Other contributors: Not specified

Version: 1

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., C1: The role of blood flow in liver lobule function and morphology, C2: Organization of the sinusoidal system and the liver lobule - referen..., C3: Zonation of metabolism and its regulation

Scales: Cell and Liver lobule

Overview preliminary results and first version of multi-scale model of human hepatic galactose metabolism.
First simulations of normal state and galactosemias.

See also:
Galactose investigation
http://seek.virtuelle-leber.de/investigations/88
Galactose study
http://seek.virtuelle-leber.de/studies/50
Galactose modelling assay
http://seek.virtuelle-leber.de/assays/71

Created: 3rd Nov 2013 at 15:03 Last updated: 8th Nov 2013 at 11:10

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