Virtual Liver SEEK Assays

We present a multi-scale model of liver galactose metabolism bridging the scales from single-cell metabolism over the tissue level to the whole-organ. The model combines a detailed kinetic model of the cellular galactose metabolism with a tissue-scale perfusion model of the sinusoid. The metabolic capacity of the whole liver is modelled by integrating the heterogeneous contribution of sinusoids differing in blood-flow rates and tissue-architecture. The model was applied to the normal physiological
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Created: 3rd Nov 2013 at 15:17 Last updated: 24th Jul 2015 at 13:30

GRN2SBML: encoding of gene regulatory network models

ID: 70

Biological problem addressed: Gene regulatory network

Investigation: 1 hidden item

Study: 1 hidden item

Models: 4 hidden items

Contributor: Sebastian Vlaic

Projects: A: Cellular level

Organisms: Not Specified

SOPs: No SOPs

Data files: GRN2SBML Bundle

Scales: Cell

No description specified

Created: 1st Nov 2013 at 10:42 Last updated: 24th Jul 2015 at 13:29

Fluidigm dynamic arrays for TaqMan® PCR

ID: 32

Assay type: Transcriptional profiling

Technology type: fluidigm high-throughput taqman platform

Investigation: 1 hidden item

Study: 1 hidden item

Contributor: Maria Thomas

Projects: A3.4: Linking signalling to metabolic functions, Showcase Steatosis

Organisms:
Homo sapiens : [Hepatocyte] (primary cell culture)

SOPs: 2 hidden items

Data files: 5 hidden items

Scales: Not specified

A technology which offers on-chip networks of microfluidc channels.This platform enables us to perform high-throughput real-time PCR with up to 9.216 data points in one run in TaqMan data quality.

Created: 6th Nov 2012 at 06:47 Last updated: 24th Jul 2015 at 12:18

Response of hepatocytes to rapid change in the medium composition (gene regulatory network)

ID: 7

Biological problem addressed: Gene expression

Investigation: Exchanging culture medium

Study: Response of hepatocytes to rapid change in the ...

Models: Response of hepatocytes to rapid change in the ...

Contributor: Data From HepatoSys

Projects: HepatoSys

Organisms:
Mus musculus : C57BL/6N (wild-type / wild-type) : [Hepatocyte] (primary cell culture)

SOPs: No SOPs

Data files: Dynamic network reconstruction identified unexp...

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
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Created: 1st Aug 2011 at 15:44 Last updated: 24th Jul 2015 at 11:50

Response of hepatocytes to rapid change in the medium composition (gene regulatory network)

ID: 6

Assay type: Gene expression profiling

Technology type: affymetrix genechip oligonucleotide arrays

Investigation: Exchanging culture medium

Study: Response of hepatocytes to rapid change in the ...

Contributor: Data From HepatoSys

Projects: HepatoSys

Organisms:
Mus musculus : C57BL/6N (wild-type / wild-type) : [Hepatocyte] (primary cell culture)

SOPs: No SOPs

Data files: Dynamic network reconstruction identified unexp...

Scales: Not specified

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: 1st Aug 2011 at 15:27 Last updated: 24th Jul 2015 at 11:48