Models

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

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
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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
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amino acid metabolism of cultured mouse hepatocytes

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

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.

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.

This is HepatoNet1 including MIRIAM annotations.

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

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

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

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
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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

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

Aminosäure-Abbau in primären Maushepatozyten

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

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
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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

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

This is just a test model for visualization in Cytoscape

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
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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.