Data files

 

Pdf 1st Announcement 7th Noordwijkerhout Symposium on Pharmocokinetics, Pharmacodynamics and Systems Pharmacology


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 8th Jul 2013 at 13:39


 

Doc Abstract_Retreat 2011


Uploader: Maria Thomas

Contributor: Maria Thomas

Other contributors: Not specified

Scales: Not specified

Nuclear Receptor PPARalpha Regulates Drug Metabolism in Human Liver

Created: 11th Nov 2011 at 15:10   Last updated: 20th Jun 2012 at 15:48


 

Zip Affymetrix microarray data of primary mouse hepatocytes, comparison of the two types of hepatocytes with high and low insulin affinity


Uploader: Clemens Kreutz

Contributor: Clemens Kreutz, María Matilde Bartolomé Rodríguez

Other contributors: Not specified

Scales: Cell

The data set was generated from four samples (mice). For each sample, three conditions were measured:
a) unsorted cells
b) sorted cells: low insulin binding type
c) sorted cells: high insuin binding type
Altogether, 4x3 =12 experimental data sets were investigated.

Gene expression profiling was performed using an AffymetrixGeneChip mouse gene 2.0 ST Array (Affymetrix Europe, Wooburn Green, UK).
The probe sequences can be downloaded from the Affymetrix website.
The following files contain probe
...

Created: 27th Mar 2014 at 09:06   Last updated: 26th Jan 2015 at 18:08


 

Png Bile canaliculi


Uploader: Seddik Hammad

Contributor: Jan Böttger, Seddik Hammad

Other contributors: Not specified

Scales: Liver lobule

reconstruction of BC network

Created: 6th Mar 2012 at 11:25   Last updated: 18th Jun 2012 at 13:58


 

Html Brownian Dynamics Simulation


Uploader: Antonia Stank

Contributor: Rebecca Wade

Other contributors: N.J. Bruce, Daria B. Kokh, M. Ozboyaci

Version: 1

Projects: F3: Kinetic data handling

Scales: Cell

Lecture notes from Winterschool in Juelich:

N.J. Bruce, Daria B. Kokh, M. Ozboyaci and Rebecca C. Wade.
Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.
In Computational Trends in Solvation and Transport in Liquids Lecture Notes, volume 28 of IAS Series, (2015) pages 259-280. Eds. Sutmann G., Grotendorst, J., Gompper,G., Marx,D. Schriften des Forschungszentrums Juelich.

https://juser.fz-juelich.de/record/188877/files/IAS-Band-28-V2.pdf

Created: 18th Sep 2015 at 13:48


 

Pdf COMBINE & ERASysAPP Tutorial 'Modelling and Simulation of Biological Models'


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: F: Data management, Virtual Liver

Scales: Not specified

Tutorial workshop outline

Created: 13th Aug 2014 at 13:25


 

Xls Computing severeness of enzymopathies


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe, Christian Bölling, Hermann-Georg Holzhütter, Matthias König, Sascha Bulik

Other contributors: Not specified

Version: 1

Projects: A: Cellular level

Scales: Cell

Supplement 5 of publication: HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

Created: 4th Mar 2014 at 11:25


 

Pdf Cytochrome P450 enzyme activity - raw data


Uploader: Bruno Christ

Contributor: Bruno Christ

Other contributors: Not specified

Scales: Liver

No description specified

Created: 12th Feb 2014 at 16:15   Last updated: 11th Jan 2016 at 08:48


 

Pdf Dynamic network reconstruction identified unexpected gene expression in primary hepatocytes after exchange of culture medium (FOSBE 2007 Contributed Paper)


Uploader: Data From HepatoSys

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

Other contributors: Not specified

Version: 1

Projects: HepatoSys

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 11:49   Last updated: 1st Aug 2011 at 13:43


 

Pdf From hepatic stellate cells to 3D Model of liver regeneration


Uploader: Iryna Ilkavets

Contributor: Frank Herweck, Iryna Ilkavets, Sonja Lukowski, Steven Dooley

Other contributors: Not specified

Scales: Not specified

Von der hepatischen Sternzelle zum 3D-Modell der Leberregeneration
In German, publication in Systembiologie 5, 2012

Created: 31st Oct 2012 at 13:01   Last updated: 10th Jun 2013 at 11:07


 

Zip GRN2SBML Bundle


Uploader: Sebastian Vlaic

Contributor: Andreas Dräger, Sebastian Vlaic

Other contributors: Michael Weber, Peter Kupfer, Bianca Hoffmann

Scales: Not specified

GRN2SBML

Copyright (c) 2012-2013 Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e.V. - Hans-Knoell-Institut (HKI).

This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation, Version 3.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
...

Created: 15th Apr 2013 at 10:59   Last updated: 1st Nov 2013 at 13:36


 

Pdf ICSB Workshop


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 22nd Jul 2014 at 11:43


 

Html ICSB Workshop copy


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 22nd Jul 2014 at 11:44


 

Pdf ICSU bio‐unions satellite symposium programme


Uploader: Martin Golebiewski

Contributor: Peter Hunter

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Not specified

No description specified

Created: 2nd Jul 2013 at 11:54


 

Ppt In vitro KD of Rab5all for 5 days followed by 30 min DiI-LDL uptake. Strong effect on LDL internalization upon Rab5 loss


Uploader: Konstantina Diamantara

Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial

Other contributors: Not specified

Scales: Not specified

No description specified

Created: 28th Feb 2014 at 11:31   Last updated: 11th Jan 2016 at 15:18


 

Ppt In vitro KD of Rab5all for 5 days. No affect on Rab11


Uploader: Konstantina Diamantara

Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial

Other contributors: Not specified

Scales: Cell, Intercellular and Liver

No description specified

Created: 28th Feb 2014 at 11:27   Last updated: 11th Jan 2016 at 15:18


 

Ppt In vitro KD of Rab5all for 5 days. Strong reduction on LAMP1 staining


Uploader: Konstantina Diamantara

Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial

Other contributors: Not specified

Scales: Cell, Intercellular and Liver

No description specified

Created: 28th Feb 2014 at 11:23   Last updated: 11th Jan 2016 at 15:18


 

Genericblue in vivo fluorescent analysis of LNP-siRNAs


Uploader: Konstantina Diamantara

Contributor: Anja Zeigerer, Jerome Gilleron, Konstantina Diamantara

Other contributors: Not specified

Scales: Not specified

No description specified

Created: 11th Dec 2013 at 10:35   Last updated: 11th Jan 2016 at 15:18


 

Genericblue KEGGViewer


Uploader: Iryna Ilkavets

Contributor: Bianca Habermann, Jose Villaveces

Other contributors: Not specified

Scales: Cell

KEGGViewer is an open-source tool freely available at the BioJS Registry. Renders a KEGGML file and displays a KEGG pathway.

Created: 19th Jun 2015 at 09:34


 

Xls Keller et al_Manuscript-relevant data


Uploader: Maria Thomas

Contributor: Andreas Dräger, Andreas Zell, Marcus Klein, Maria Thomas, Roland Keller, Thomas Joos, Ulrich Zanger, Ute Metzger, Wolfgang E. Thasler

Other contributors: Not specified

Scales: Not specified

Contains all experimental data used for the study "Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy logic modeling" by Keller and colleagues.

Created: 6th Oct 2015 at 13:16


 

Html LigDig webserver


Uploader: Jonathan Fuller

Contributor: Jonathan Fuller, Michael Martinez, Rebecca Wade

Other contributors: Not specified

Scales: Not specified

LigDig is a web application for investigating ligand-protein interactions. LigDig can be used to query structural and functional properties. LigDig can be accessed at http://mcm.h-its.org/ligdig

Created: 17th Jan 2014 at 15:21   Last updated: 6th Dec 2014 at 18:09


 

Zip Microarray data from transgenic SLC mice


Uploader: Madlen Matz-Soja

Contributor: Madlen Matz-Soja, Rolf Gebhardt, Wolfgang Schmidt-Heck

Other contributors: Not specified

Version: 2

Projects: A1: Cellular metabolism

Scales: Cell

Transgenic mice with a conditional hepatocyte-specific deletion of the Smoothened gene after adolescence were characterized for alterations in gene expression via microarrays.

Created: 20th Oct 2015 at 09:10   Last updated: 3rd May 2017 at 11:12


 

Ppt Modeling approaches in A3.4 and B5


Uploader: Andreas Dräger

Contributor: Andreas Dräger

Other contributors: Not specified

Scales: Not specified

The project A3.4 will create a combined model that containes metabolism, gene regulation and signal transduction with main focus on the influence of the nuclear receptors PXR, CAR, and PPARa. To this end, information is gathered from HepatoNet1, TRANSFAC, and Ingenuity aiming at creating an overal model, which will be equipped with kinetic information subsequently. In project B.5 a model of IL6 signal transduction that links of STAT3 and MAPK (ERK) to ADME genes is created using TRANSFAC, Ingenuity,
...

Created: 25th Jun 2011 at 11:23   Last updated: 12th Jan 2016 at 08:13


 

Pdf NORMSYS/ISBE Workshop: Standards for Data and Model Exchange in Systems Biology


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Not specified

Workshop outline

Created: 18th Jul 2014 at 11:48


 

Xls One-Meal and three-meal glucose timecourse [Stanhope2008]


Uploader: Matthias König

Contributor: Matthias König

Other contributors: Not specified

Version: 1

Projects: A: Cellular level

Scales: Not specified

Experimental data digitized from publication figure.

Twenty-four-hour endocrine and metabolic profiles following consumption of high-fructose corn syrup-, sucrose-, fructose-, and glucose-sweetened beverages with meals.
Stanhope KL, Griffen SC, Bair BR, Swarbrick MM, Keim NL, Havel PJ.
Am J Clin Nutr. 2008 May;87(5):1194-203.
PMID: 18469239
http://www.ncbi.nlm.nih.gov/pubmed/18469239

Created: 30th Jun 2015 at 07:18


 

Pdf Programme German Conference on Bioinformatics 2012 Satellite Workshop Organ-oriented Systems Biology


Uploader: Dominik Driesch

Contributor: Dominik Driesch

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 1st Nov 2012 at 16:44


 

Genericblue PsicquicGraph


Uploader: Iryna Ilkavets

Contributor: Bianca Habermann, Jose Villaveces

Other contributors: Not specified

Scales: Cell

PsicquicGraph, a BioJS component to visualize molecular inteactions from PSICQUIC servers. PsicquicGraph is freely available at the BioJS Registry for download and enhancement. Instructions on how to use the tool are available here http://goo.gl/kDaIgZ and the source code can be found at http://github.com/biojs/biojs and DOI:10.5281/zenodo.7709

Created: 19th Jun 2015 at 09:46


 

Html SABIO-RK


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 22nd Jul 2014 at 11:41


 

Html SDA7


Uploader: Antonia Stank

Contributor: Rebecca Wade

Other contributors: Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter

Scales: Cell

SDA7 can be used to carry out Brownian dynamics simulations of the diffusional association in a continuum aqueous solvent of two solute molecules, e.g. proteins, or of a solute molecule to an inorganic surface. SDA7 can also be used to simulate the diffusion of multiple proteins, in dilute or concentrated solutions, e.g., to study the effects of macromolecular crowding.

Created: 18th Sep 2015 at 14:51


 

Xls SEEK test


Uploader: Lorenza D'Alessandro

Contributor: No Contributor

Other contributors: Not specified

Scales: Not specified

No description specified

Created: 28th Nov 2012 at 08:58   Last updated: 28th Nov 2012 at 09:07


 

Genericblue Semantic EvidencE (SEE)


Uploader: Iryna Ilkavets

Contributor: Christian Bölling, Hermann-Georg Holzhütter, Michael Weidlich

Other contributors: Not specified

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Not specified

SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques. Link to the project is given.

Created: 19th Jun 2015 at 10:19


 

Pdf Supplement to "A Conceptual Mathematical Model of the Dynamic Self-Organisation of Distinct Cellular Organelles"


Uploader: Bernd Binder

Contributor: Bernd Binder

Other contributors: Not specified

Version: 1

Projects: A3.3: Hepatocyte polarity

Scales: Cell

No description specified

Created: 13th Jan 2014 at 13:08   Last updated: 13th Jan 2014 at 13:15


 

Pdf Supplement to A Hypothetical Model of Cargo-Selective Rab Recruitment During Organelle Maturation


Uploader: Bernd Binder

Contributor: Bernd Binder

Other contributors: Not specified

Version: 1

Projects: A3.3: Hepatocyte polarity

Scales: Not specified

No description specified

Created: 13th Jan 2014 at 13:12


 

Zip Supplementary data to Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Enzyme protein chain lengths

Created: 10th Jan 2014 at 11:21   Last updated: 16th Jan 2014 at 16:42


 

Pdf Supplementary table 1 to Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 10th Jan 2014 at 11:20   Last updated: 16th Jan 2014 at 16:43


 

Pdf Supplementary table 2 to Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 10th Jan 2014 at 11:20   Last updated: 16th Jan 2014 at 16:44


 

Pdf Supplementary table 3 to Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 10th Jan 2014 at 11:20   Last updated: 16th Jan 2014 at 16:44


 

Pdf Supplementary table 4 to Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Uploader: Andreas Hoppe

Contributor: Andreas Hoppe

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 10th Jan 2014 at 11:20   Last updated: 16th Jan 2014 at 16:41


 

Xls test parsing hünfeld


Uploader: Meik Bittkowski

Contributor: Martin Golebiewski, Meik Bittkowski

Other contributors: Not specified

Version: 1

Projects: F: Data management

Scales: Not specified

No description specified

Created: 30th Oct 2013 at 11:07   Last updated: 13th Apr 2016 at 13:33


 

Pdf TGF-β induced hepatocellular Wisp1 is expressed in HCC and drives proliferation of epithelial type cancer cells


Uploader: Iryna Ilkavets

Contributor: Iryna Ilkavets, Steven Dooley

Other contributors: Not specified

Scales: Cell, Intercellular and Liver lobule

Invited conference talk at Cold Spring Harbour Asia Meeting Shuzou 2012 Liver Metabolism, Diseases & Cancer

Created: 31st Oct 2012 at 12:52   Last updated: 10th Jun 2013 at 11:10


 

Pdf Urea synthesis rate - raw data


Uploader: Bruno Christ

Contributor: Bruno Christ

Other contributors: Not specified

Scales: Liver

No description specified

Created: 12th Feb 2014 at 16:18   Last updated: 11th Jan 2016 at 08:50


 

Xml Vascular patterning (Morpheus model)


Uploader: Walter De Back

Contributor: Walter De Back

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Morpheus XML model of patterning of HUVEC cells in Matrigel culture, based on retention of external VEGF to cell-modified matrix.

As used in reference:
A Köhn-Luque, W de Back, Y Yamaguchi, K Yoshimura, M A Herrero, T Miura (2013) Dynamics of VEGF matrix-retention in vascular network patterning, Physical Biology, 10(6) : 066007, doi: 10.1088/1478-3975/10/6/066007

Created: 24th Jan 2014 at 14:08


 

Pdf Virtual Liver Retreat 2012: Quantitative Proteomics of liver


Uploader: S. Babak Azimifar

Contributor: Matthias Mann, S. Babak Azimifar

Other contributors: Not specified

Scales: Cell and Liver

Virtual Liver Retreat 2012 (Poster)
Quantitative Proteomics of liver

S. Babak Azimifar, Kirti Sharma, Mara Monetti, Nagarjuna Nagaraj and Matthias Mann*.
*Corresponding author; contact: S. Babak Azimifar (Max Planck Institute of Biochemistry, Martinsried, Germany; Azimifar@biochem.mpg.de).

Despite enormous progress in MS based proteomics, accurate quantification of in vivo proteomic and phosphoproteomic changes such as those in liver remains a challenge. We developed a new strategy which we termed
...

Created: 28th Nov 2012 at 08:35   Last updated: 28th Nov 2012 at 09:28


 

Html webSDA


Uploader: Antonia Stank

Contributor: Jonathan Fuller, Rebecca Wade

Other contributors: Xiaofeng Yu, Michael Martinez, Annika L. Gable, Neil J. Bruce, Stefan Richte

Scales: Cell

webSDA: a web server to simulate macromolecular diffusional association.

Created: 18th Sep 2015 at 14:47   Last updated: 18th Sep 2015 at 14:48


 

Doc Working with biological networks in VLN


Uploader: Jose Villaveces

Contributor: Jose Villaveces

Other contributors: Not specified

Scales: Not specified

The use of biological networks for interpreting data is becoming a standard in bioinformatics analysis. It enables us to look at a process from the perspective of pathways and network modules rather than single genes. Yet, there are still many obstacles when dealing with biological networks, such as protein-protein interaction or genetic networks. Firstly, these type of networks represent binary, rather than complex biological interactions; then, networks are still viewed as ‘static’ and do not
...

Created: 19th Oct 2011 at 16:14   Last updated: 21st Oct 2011 at 11:22



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