Models

 

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 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 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 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 AminoAcidMetabolism_Liver


Uploader: Data From HepatoSys

Contributor: Data From HepatoSys, Reinhard Guthke, Rolf Gebhardt, Sebastian Zellmer, Wolfgang Schmidt-Heck

Other contributors: H. Buentemeyer, D. Teupser, J. Thiery

Model type: Not specified

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Mus musculus

Environment: Not specified

Scales: Cell

amino acid metabolism of cultured mouse hepatocytes

Created: 25th Jul 2011 at 15:09   Last updated: 24th Feb 2012 at 15:26


 

Kformula Endocytosis


Uploader: Data From HepatoSys

Contributor: Andreas Deutsch, Data From HepatoSys, Lutz Brusch, Marino Zerial, Yannis Kalaidzidis

Other contributors: Perla Del Conte-Zerial, Jochen C Rink, Claudio Collinet

Model type: Not specified

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Not specified

Environment: Not specified

Scales: Cell

GTPases of the Rab family provide a molecular ID code to the generation, maintenance and transport of intracellular compartments. Here, we addressed the molecular design principles of endocytosis by focusing on the conversion of early endosomes into late endosomes, which entails replacement of Rab5 by Rab7. We demonstrate that intermodule interactions share similarities with the toggle switch described for the cell cycle. However, Rab5-to-Rab7 conversion is rather based on a newly characterized
...

Created: 29th Jul 2011 at 17:13   Last updated: 24th Feb 2012 at 14:08


 

Kformula Endocytosis: Rab5 domain formation on the early endosome (Rab5PDE)


Uploader: Data From HepatoSys

Contributor: Andreas Deutsch, Bianca Habermann, Data From HepatoSys, Lutz Brusch, Marino Zerial, Yannis Kalaidzidis

Other contributors: Perla Del Conte-Zerial, Jochen Rink

Model type: Partial differential equations (PDE)

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Not specified

Environment: Not specified

Scales: Cell

This model describes a core process during endocytosis. Intracellular vesicles called early endosomes contain the endocytosed cargo, e.g. signaling components like growth factors and RTKs, pathogens like viruses and nutrients like iron in transferrin. Early endosomes form an interacting pool of thousands of vesicles and jointly constitute the sorting and transport machinery in the endocytic pathway. Together with the cargo, membrane components travel to other compartments of the pathway which
...

Created: 1st Aug 2011 at 18:11   Last updated: 24th Feb 2012 at 16:55


 

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 hepatoModel (stoichiometric model of the hepatocyte metabolism) L2V1


Uploader: Data From HepatoSys

Contributor: Andreas Hoppe, Christian Bölling, Data From HepatoSys, Hermann-Georg Holzhütter, Matthias König, Michael Weidlich, Sascha Bulik

Other contributors: Sabrina Hoffmann, Katrin Hübner, Anja Karlstädt, Ramanan Ganeshan, Kristian Rother, Jörn Behre

Model type: Stoichiometric model

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Homo sapiens

Environment: Not specified

Scales: Cell

This xml contains the current stoichiometric model on the 6th of november 2008. It is a subnetwork of hepatoNet where all blocked reactions (with respect to our simulation conditions) are removed. This model is ready to use, fulfills already 80% of the hepatocyte functions we intend to include in our model. However, LDL synthesis is not yet realized in this version. We use our proper Identifiers, so if you need a mapping to public ones (e.g. KEGG), contact us.

Created: 27th Jul 2011 at 16:44   Last updated: 24th Feb 2012 at 15:06


 

Kformula hepatoNet (stoichiometric network of the hepatocyte metabolism) L2V3


Uploader: Data From HepatoSys

Contributor: Andreas Hoppe, Christian Bölling, Data From HepatoSys, Hermann-Georg Holzhütter, Matthias König, Michael Weidlich, Sascha Bulik

Other contributors: Sabrina Hoffmann, Katrin Hübner, Anja Karlstädt, Ramanan Ganeshan, Kristian Rother, Jörn Behre

Model type: Stoichiometric model

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Homo sapiens

Environment: Not specified

Scales: Cell

This xml contains the current stoichiometric network on the 6th of november 2008. It contains all reactions we found to exist in liver until now. We use our proper Identifiers, so if you need a mapping to public ones (e.g. KEGG), contact us.

Created: 27th Jul 2011 at 17:10   Last updated: 24th Feb 2012 at 15:09


 

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 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 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 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 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 Model TCA, electrophysiological transmembran potential & respiratory chain


Uploader: Sascha Bulik

Contributor: Hermann-Georg Holzhütter, Nikolaus Berndt, Sascha Bulik

Other contributors: Not specified

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Version: 1

Projects: A1: Cellular metabolism

Organism: Homo sapiens

Environment: Not specified

Scales: Cell

The model comprises the reactions of the citric acid cycle, the respiratory chain, oxidative phosphorylation, mitochondrial ATP generation, the exchange of adenine nucleotides exchange between mitochondrial matrix and cytosol, as well as the transport of small ions across the inner mitochondrial membrane.
The respiratory chain complexes I and III are modelled in high resolution providing insight into electron occupation states of ROS generating sites depending on energetic challenge and enzyme
...

Created: 5th Nov 2012 at 09:45   Last updated: 5th Nov 2012 at 09:45


 

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 Morpheus: modeling environment for multicellular systems biology


Uploader: Walter De Back

Contributor: Andreas Deutsch, Lutz Brusch, Walter De Back

Other contributors: Not specified

Model type: Not specified

Model format: Not specified

Scales: Cell, Intercellular and Liver lobule

Morpheus is the modeling environment for multicellular systems biology developed at the IMC group (prof. Andreas Deutsch) at the Center for High Performance Computing at the the Technische Universität Dresden.

See: http://imc.zih.tu-dresden.de/wiki/morpheus

Created: 23rd Oct 2012 at 13:08   Last updated: 4th Dec 2012 at 13:35


 

Kformula MW-AA_version12_abbau


Uploader: Data From HepatoSys

Contributor: Data From HepatoSys, Reinhard Guthke, Rolf Gebhardt, Sebastian Zellmer, Wolfgang Schmidt-Heck

Other contributors: Not specified

Model type: Not specified

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Mus musculus

Environment: Not specified

Scales: Cell

Aminosäure-Abbau in primären Maushepatozyten

Created: 1st Aug 2011 at 12:16   Last updated: 24th Feb 2012 at 15:25


 

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


 

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 Response of hepatocytes to rapid change in the medium composition (gene regulatory network): Model 1100 freshMedia


Uploader: Data From HepatoSys

Contributor: Data From HepatoSys, Reinhard Guthke, Rolf Gebhardt, Sebastian Zellmer, Wolfgang Schmidt-Heck

Other contributors: Not specified

Model type: Not specified

Model format: SBML

Version: 1

Projects: HepatoSys

Organism: Mus musculus

Environment: Not specified

Scales: Cell

Primary hepatocytes were exposed to a stimulus by exchanging culture medium, thereby simulating changes in the blood composition. The expression of genes at different time points was recorded. Differentially expressed genes were clustered using fuzzy c-means algorithm into five groups. The arcs of the possible network were identified using the NetGenerator algorithm under the restriction of biological knowledge. The analysis was restricted to the main metabolic pathways of hepatocytes. The reverse
...

Created: 25th Jul 2011 at 14:48   Last updated: 24th Feb 2012 at 15:11


 

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 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 Testmodel Cytoscape


Uploader: Martin Golebiewski

Contributor: Jonathan Fuller, Martin Golebiewski

Other contributors: Not specified

Model type: Graphical model

Model format: XGMML

Version: 2

Projects: F1: The data management system

Organism: Not specified

Environment: Cytoscape Web

Scales: Cell

This is just a test model for visualization in Cytoscape

Created: 22nd May 2012 at 16:01   Last updated: 1st Oct 2012 at 15:51


 

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 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



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