Models

 

Kformula Kinetic Model of Hepatic Glucose Metabolism


Uploader: Matthias König

Contributor: Hermann-Georg Holzhütter, Matthias König, Sascha Bulik

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SBML

Scales: Cell and Liver

Despite the crucial role of the liver in glucose homeostasis, a detailed mathematical
model of human hepatic glucose metabolism is lacking so far. Here we present a
detailed kinetic model of glycolysis, gluconeogenesis and glycogen metabolism in
human hepatocytes integrated with the hormonal control of these pathways by insulin,
glucagon and epinephrine. Model simulations are in good agreement with experimental
data on (i) the quantitative contributions of glycolysis, gluconeogenesis, and glycogen
...

Created: 14th Mar 2012 at 00:59   Last updated: 16th Feb 2017 at 12:12


 

Kformula HepatoNet1 annotated


Uploader: Andreas Dräger

Contributor: Andreas Dräger, Roland Keller, Stephanie Hoffmann

Other contributors: Not specified

Model type: Stoichiometric model

Model format: SBML

Version: 1

Projects: A1: Cellular metabolism

Organism: Homo sapiens

Environment: Not specified

Scales: Cell

This is HepatoNet1 including MIRIAM annotations.

Created: 23rd Mar 2012 at 11:41   Last updated: 12th Jan 2016 at 08:13


 

Kformula Human Geometric Liver Model


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen

Other contributors: Not specified

Model type: Not specified

Model format: Not specified

Version: 1

Projects: No Projects

Organism: Homo sapiens

Environment: Not specified

Scales: Liver

supplementary information for L. O. Schwen, A. Schenk, C. Kreutz, J. Timmer, M. M. Bartolomé-Rodriguez, L. Kuepfer, and T. Preusser: Representative Sinusoids For Hepatic Four-Scale Pharmacokinetics Simulations, PLoS ONE, 10(7):e0133653, 1-39, 2015, DOI 10.1371/journal.pone.0133653

Created: 30th Jul 2015 at 09:25


 

Kformula Simplified model of hepatic glucose metabolism used for perfusion integration


Uploader: Matthias König

Contributor: Matthias König

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Version: 1

Projects: A: Cellular level

Organism: Not specified

Environment: Not specified

Scales: Cell

For detailed description see:
Biomech Model Mechanobiol. 2015 Jun;14(3):515-36. doi: 10.1007/s10237-014-0619-z. Epub 2014 Sep 19.
Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach.
Ricken T1, Werner D, Holzhütter HG, König M, Dahmen U, Dirsch O.
http://www.ncbi.nlm.nih.gov/pubmed/25236798

Created: 30th Jun 2015 at 07:24


 

Kformula The JSBML project


Uploader: Andreas Dräger

Contributor: Andreas Dräger

Other contributors: Not specified

Model type: Not specified

Model format: SBML

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

Created: 23rd Jun 2015 at 21:05


 

Kformula A description of a detailed ordinary differential equation (ODE) model of Wnt/β-catenin signalling


Uploader: Iryna Ilkavets

Contributor: Andreas Hecht

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: PDF (Model description)

Scales: Cell

It is a link to a supplementary information from a publication: Benary, U., Kofahl, B., Hecht, A. and Wolf, J. (2015), Mathematical modelling suggests a differential impact of β-transducin repeat-containing protein paralogues on Wnt/β-catenin signalling dynamics. FEBS Journal, 282: 1080–1096. doi: 10.1111/febs.13204

http://onlinelibrary.wiley.com/doi/10.1111/febs.13204/suppinfo

The Wnt/β-catenin signalling pathway is involved in the regulation of a multitude of cellular processes by controlling
...

Created: 15th Jun 2015 at 13:22   Last updated: 15th Jun 2015 at 14:19


 

Kformula PBPK model of CFDA


Uploader: Markus Krauß

Contributor: Lars Küpfer, Lars Ole Schwen, Markus Krauß

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SXML

Scales: Not specified

No description specified

Created: 25th Oct 2013 at 15:22   Last updated: 6th May 2015 at 08:08


 

Kformula PBPK model of midazolam


Uploader: Markus Krauß

Contributor: Lars Küpfer, Lars Ole Schwen, Markus Krauß

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SXML

Scales: Organism

No description specified

Created: 25th Oct 2013 at 15:11   Last updated: 6th May 2015 at 08:08


 

Kformula PBPK model of spiramycin


Uploader: Markus Krauß

Contributor: Lars Küpfer, Lars Ole Schwen, Markus Krauß

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SXML

Scales: Organism

No description specified

Created: 24th Oct 2013 at 16:56   Last updated: 6th May 2015 at 08:08


 

Kformula Mobi PBPK Models of Paracetamol, Ammonia and Allopurinol


Uploader: Markus Krauß

Contributor: Jörg Lippert, Lars Küpfer, Markus Krauß

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SXML

Version: 1

Projects: E4: Vertical integration across biological scales, E: Model integration

Organism: Homo sapiens

Environment: MoBi

Scales: Organism

Mobi PBPK Models of Paracetamol, Ammonia and Allopurinol, relating to Publication Krauss et al (2012) in PLoS Comp Biol

Created: 30th Oct 2012 at 09:09   Last updated: 6th May 2015 at 08:07


 

Kformula Mathematical model for liver size regulation by N. Hohmann, W. Weiwei, U. Dahmen, O. Dirsch, A. Deutsch, A. Voss-Böhme


Uploader: Lutz Brusch

Contributor: Andreas Deutsch, Anja Voß–Böhme, Nadine Hohmann, Olaf Dirsch, Uta Dahmen, Weiwei Wei

Other contributors: Not specified

Model type: Not specified

Model format: Not specified

Scales: Liver lobule and Liver

Model has been published in Hohmann et al., PLoS ONE 9(4): e93207 (2014), doi: 10.1371/journal.pone.0093207

Created: 24th Jan 2014 at 14:33   Last updated: 17th Jun 2014 at 11:42


 

Kformula Geometric models of murine liver and vascular systems


Uploader: Lars Ole Schwen

Contributor: Andrea Schenk, Fabian Kiessling, Lars Ole Schwen

Other contributors: Felix Gremse

Model type: Not specified

Model format: Not specified

Version: 1

Projects: No Projects

Organism: Mus musculus

Environment: Not specified

Scales: Liver

used for the publication "Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver"

Created: 14th Mar 2014 at 09:19   Last updated: 14th Mar 2014 at 09:19


 

Kformula A hypothetical model of cargo-selective rab recruitment during organelle maturation.


Uploader: Bernd Binder

Contributor: Bernd Binder

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Version: 1

Projects: A3.3: Hepatocyte polarity

Organism: Not specified

Environment: Not specified

Scales: Not specified

Rabs constitute a group of small GTPases that confer directionality to intracellular vesicle transport by promoting on the membrane of transport vesicles in the formation of specific protein complexes allowing for efficient fusion with a selected set of target organelles. The molecular mechanism controlling recruitment of the correct Rab at the right time is not fully understood. We propose a model according to which the residence time of a given Rab on the membrane of an organelle is determined
...

Created: 30th Jan 2014 at 11:17   Last updated: 30th Jan 2014 at 11:17


 

Kformula A Conceptual Mathematical Model of the Dynamic Self-Organisation of Distinct Cellular Organelles


Uploader: Bernd Binder

Contributor: Bernd Binder, Hermann-Georg Holzhütter, Nikolaus Berndt

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Version: 1

Projects: A3.3: Hepatocyte polarity

Organism: Not specified

Environment: Not specified

Scales: Cell

Formation, degradation and renewal of cellular organelles is a dynamic process based on permanent budding, fusion and inter-organelle traffic of vesicles.

Created: 30th Jan 2014 at 11:07   Last updated: 30th Jan 2014 at 11:07


 

Kformula Morpheus model of Smo regulation in response to Hh


Uploader: Lutz Brusch

Contributor: Lutz Brusch

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Version: 1

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Organism: Not specified

Environment: Not specified

Scales: Cell

Morpheus model of Smo regulation in response to Hh

As used in refereence:
A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 doi: 10.1242/​jcs.128926

Created: 28th Jan 2014 at 10:17   Last updated: 28th Jan 2014 at 10:18


 

Kformula SBML model of Smo regulation in response to Hh


Uploader: Lutz Brusch

Contributor: Lutz Brusch

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SBML

Version: 1

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Organism: Not specified

Environment: Not specified

Scales: Cell

SBML model of Smo regulation in response to Hh

As used in refereence:
A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 doi: 10.1242/​jcs.128926

Created: 28th Jan 2014 at 10:13


 

Kformula A community-driven global reconstruction of human metabolism.


Uploader: Martin Golebiewski

Contributor: Andreas Hoppe, Christian Bölling, Nicolas Le Novère

Other contributors: Not specified

Model type: Not specified

Model format: SBML

Version: 1

Projects: A: Cellular level, HepatoSys, Virtual Liver

Organism: Homo sapiens

Environment: Not specified

Scales: Cell

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ∼2× more reactions and ∼1.7× more unique metabolites. Using Recon 2 we predicted
...

Created: 27th Nov 2013 at 10:35


 

Kformula HepatoNet 1b with mouse gene annotations


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe, Hermann-Georg Holzhütter

Other contributors: Not specified

Model type: Stoichiometric model

Model format: SBML

Version: 1

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Organism: Mus musculus

Environment: Not specified

Scales: Cell

No description specified

Created: 11th Feb 2013 at 14:44


 

Kformula TGFbeta Signalling Feedback Loops


Uploader: Martin Golebiewski

Contributor: Anastasia Bachmann, Christoph Meyer, Philippe Lucarelli, Steven Dooley, Sven Sahle, Ursula Klingmüller, Ursula Kummer

Other contributors: Katja Wegner, Jan-Ulrich Schad, Peter Nickel

Model type: Ordinary differential equations (ODE)

Model format: SBML

Version: 1

Projects: Virtual Liver

Organism: Mus musculus

Environment: Copasi

Scales: Cell

Transforming growth factor β (TGF-β) ligands activate a signaling cascade with multiple cell context dependent outcomes. Disruption or disturbance leads to variant clinical disorders. To develop strategies for disease intervention, delineation of the pathway in further detail is required. Current theoretical models of this pathway describe production and degradation of signal mediating proteins and signal transduction from the cell surface into the nucleus, whereas feedback loops have not
...

Created: 5th Feb 2013 at 18:28   Last updated: 5th Feb 2013 at 18:33


 

Kformula NFkappaB signalling in primary hepatocytes


Uploader: Katharina Beuke

Contributor: Katharina Beuke, Sven Sahle, Ursula Kummer

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: SBML

Scales: Cell

We created an ODE-based model of TNFalpha-induced NFkappaB signalling in primary hepatocytes.

Created: 19th Oct 2012 at 17:26   Last updated: 10th Jan 2013 at 10:18



Log in / Register

Need an account?
Sign up

Forgotten password?

Front Page

Virtual Liver Network

(v.0.22.0)

Related Projects and friends


Imprint Taverna workflow workbench myExperiment JWS Online ISATAB myGrid Sabio-RK BioPortal Semantic SBML

Powered by:

Ror-logo-32

Icons:
Silk icons 1.3
Crystal Clear icons