Presentations

 

Tar another test


Uploader: Quyen Nguyen

Contributor: Quyen Nguyen

Other contributors: Not specified

Version: 2

Projects: No Projects

Scales: Not specified

No description specified

Created: 2nd Jun 2016 at 14:54   Last updated: 3rd Jun 2016 at 10:25


 

Pdf LigDig: a web server for querying ligand–protein interactions


Uploader: Antonia Stank

Contributor: Antonia Stank, Jonathan Fuller, Michael Martinez, Rebecca Wade

Other contributors: Stefan Henrich, Stefan Richter

Scales: Not specified

Background: One of the major challenges in complex multi-disciplinary systems biology projects is to understand and process data from a wide variety of data sources. Computational tools to assist in the analysis of this data are essential.
Method: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is
...

Created: 15th Jan 2016 at 13:49


 

Zip Multi-Scale Simulation of Heterogeneous Metabolism in Mammalian Livers


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen

Other contributors: Felix Gremse, Markus Krauss, Christoph Niederalt

Scales: Cell, Liver lobule, Liver and Organism

Talk at Jena Centre for Bioinformatics, 2014-11-20

Created: 25th Nov 2014 at 17:37


 

Genericblue Multiscale Simulation of Zonated Metabolism in Steatotic Livers


Uploader: Lars Ole Schwen

Contributor: André Homeyer, Arne Schenk, Lars Küpfer, Lars Ole Schwen, Michael Schwier, Olaf Dirsch, Tobias Preusser, Uta Dahmen

Other contributors: Felix Gremse

Scales: Cell, Liver lobule, Liver and Organism

Presentation at VPH 2014

Created: 11th Sep 2014 at 09:50


 

Zip Spatio-Temporal Simulation of First Pass Drug Perfusion in a Murine Liver


Uploader: Lars Ole Schwen

Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser

Other contributors: Christoph Niederalt, Felix Gremse

Scales: Cell, Liver lobule and Organism

Talk given at ISGSB 2014 in Durham (UK)

Created: 8th Sep 2014 at 10:03


 

Zip Spatially Resolved Simulation of Glucose Metabolism in the Human Liver


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen, Matthias König, Tobias Preusser

Other contributors: Not specified

Scales: Cell, Liver lobule, Liver and Organism

Presentation at WCCM-ECCM-ECFD 2014

Created: 25th Jul 2014 at 16:01


 

Genericblue Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver


Uploader: Lars Ole Schwen

Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser

Other contributors: Christoph Niederalt, Felix Gremse

Scales: Cell, Liver and Organism

Poster for VLN Retreat 2013 in Hünfeld

Created: 23rd Oct 2013 at 14:05   Last updated: 12th Jun 2014 at 09:58


 

Pdf Multi-Scale Simulation of Zonated Liver Metabolism


Uploader: Lars Ole Schwen

Contributor: Ahmed Ghallab, Andrea Schenk, André Homeyer, Arne Schenk, Fabian Kiessling, Hermann-Georg Holzhütter, Jan Georg Hengstler, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Serene Lee, Tobias Preusser, Uta Dahmen, Ute Hofmann

Other contributors: Felix Gremse, Benjamin Knowles

Scales: Cell, Liver lobule, Liver and Organism

presentation at SBMC2014

Created: 14th May 2014 at 15:30   Last updated: 14th May 2014 at 15:55


 

Pdf How to prepare an input for the Portal?


Uploader: Iryna Ilkavets

Contributor: Iryna Ilkavets, Ivan Savora, Martin Golebiewski, Meik Bittkowski, Wolfgang Müller

Other contributors: Not specified

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

The Portal:
6 dimensions to organize content
easy information about difficult topics
quick and easy to publish the input
visibility to the public, colleagues and funders
presentation of the work of group

Created: 8th May 2014 at 15:24


 

Pdf GTC Bio - Protein-protein interaction October 23rd-25th Invited talk


Uploader: Jonathan Fuller

Contributor: Jonathan Fuller

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Invited talk abstract:

Recent successes have challenged the widely held belief that protein-protein interactions (PPIs) are 'undruggable'. We show that binding pockets defining PPIs and those that define protein-ligand interactions of currently marketed drugs are markedly different. In the case of PPIs, drug discovery methods that simultaneously target several small pockets at the protein-protein interface are likely to increase the chances of success in this new and important field of therapeutics.
...

Created: 18th Dec 2013 at 12:40


 

Genericblue ChemSpot


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

ChemSpot is a named entity recognition tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and IUPAC entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It currently achieves an F1 measure of 74.2% on the SCAI corpus.
ChemSpot is released under the Common Public License 1.0.
...

Created: 16th Dec 2013 at 10:23


 

Pdf Extended Feature Set for Chemical Named Entity Recognition and Indexing


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber, Philippe Thomas

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

The BioCreative IV CHEMDNER Task provides participants with the opportunity to compare their methods for chemical named entity recognition (NER) and indexing in a controlled environment. We contributed to this task with our previous conditional random field based system [1] extended by a number of novel general and domain-speci c features. For the latter, we used features derived from two existing chemical NER systems, ChemSpot [2] and OSCAR [3], as well as various external resources. In this
...

Created: 16th Dec 2013 at 10:01


 

Pdf WBI-NER: The impact of domain-specific features on the performance of identifying and classifying mentions of drugs


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

Named entity recognition (NER) systems are often based on machine learning techniques to reduce the labor-intensive development of hand-crafted extraction rules and domain-dependent dictionaries. Nevertheless, time-consuming feature engineering is often needed to achieve state-of-the-art performance. In this study, we investigate the impact of such domain-specific features on the performance of recognizing and classifying mentions of pharmacological substances. We compare the performance of a
...

Created: 16th Dec 2013 at 09:53


 

Pdf The Challenges of 21st Century Medicine Demand a Big Science Approach


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Talk given at the Transatlantic Science Forum meeting in the European Parliament, November 12, 2013 (see http://www.tsciencef.org/event.php?id=2)

Created: 15th Nov 2013 at 15:43


 

Pdf Presentation: From Hepatocytes to Whole Liver Function: A Multi-scale Model of Human Galactose Metabolism (VLN Retreat 2013)


Uploader: Matthias König

Contributor: Hermann-Georg Holzhütter, Matthias König

Other contributors: Not specified

Scales: Cell and Liver lobule

Overview preliminary results and first version of multi-scale model of human hepatic galactose metabolism.
First simulations of normal state and galactosemias.

See also:
Galactose investigation
http://seek.virtuelle-leber.de/investigations/88
Galactose study
http://seek.virtuelle-leber.de/studies/50
Galactose modelling assay
http://seek.virtuelle-leber.de/assays/71

Created: 3rd Nov 2013 at 15:03   Last updated: 8th Nov 2013 at 11:10


 

Pdf Uncertainty of model predictions


Uploader: Clemens Kreutz

Contributor: Andreas Raue, Clemens Kreutz, Jens Timmer, Ursula Klingmüller

Other contributors: Not specified

Scales: Not specified

Poster presented at the VLN Retreat in Hünfeld 2013
A method for statistically assessing uncertainties of model predictions is presented.

Created: 30th Oct 2013 at 11:01


 

Pdf Moving Towards a Unified Protein Interaction Network


Uploader: Jose Villaveces

Contributor: Bianca Habermann, Jose Villaveces

Other contributors: Rafael C. Jimenez

Scales: Not specified

The analysis of biological networks for interpreting data is becoming a standard in bioinformatics as it enables us to look at a process from the perspective of pathways and network modules rather than single proteins. To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.
We work on several aspects concerning data integration in protein interaction
...

Created: 30th Oct 2013 at 10:07   Last updated: 30th Oct 2013 at 10:21


 

Pdf Constructive Algorithms for Modeling Realistic Vascular Structures


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen, Tobias Preusser

Other contributors: Not specified

Scales: Liver

Presentation at ECMTB 2011

Created: 8th Jul 2011 at 09:46   Last updated: 23rd Oct 2013 at 13:58


 

Pdf ICSB Tutorial: SABIO-RK - Reaction Kinetics Database


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: F3: Kinetic data handling

Scales: Not specified

No description specified

Created: 9th Sep 2013 at 12:12


 

Pdf ICSB workshop programme


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

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

No description specified

Created: 8th Jul 2013 at 09:52



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