Bioinformatics

Bioinformatics

The cooperation between the Genetic Epidemiology, Medical University Innsbruck (Univ.-Prof Florian Kronenberg) and the Research Group Databases and Information Systems  (DBIS, Univ.-Prof Günther Specht) already started in 2007. The overall goal of the cooperation is to find new ways of storing and processing big data derived from Next Generation Sequencing (NGS) using RDBMS as well as NoSql Systems. Parallelization strategies like MapReduce, usability of developed systems and reproducability of results are two major aspects within the cooperation. Several research projects have been accomplished so far.

An updated list on our projects can be found at the website of the Division of Genetic Epiemdiology.

Cloudgene

Cloudgene is an open-source platform to improve the usability of MapReduce programs by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house and rented clusters, i.e. in the cloud. The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface.
http://cloudgene.uibk.ac.at

Haplogrep

HaploGrep is implemented as a web application based on Phylotree, a periodically updated classification tree estimated from data worldwide. Any given range of the mitochondrial genome can be used for haplogroup classification, which is based on the phylogenetic stability of mtDNA polymorphisms. For every input sample the top ten results and the phylogenetic position of the respective haplogroup are displayed, thus providing a detailed explanation how and why a haplogroup was ranked best. HaploGrep generates an interactive data visualization of the results and provides recommendations which polymorphisms should be analyzed additionally to get a more accurate result. HaploGrep can be used without login and imported samples are exclusive visible to appropriate users due to HaploGrep s session management. The export possibilities as a standard tab delimited file and as a *.rdf file for the phylogenetic software network.exe render HaploGrep the currently best solution for human mtDNA haplogroup determination.
http://haplogrep.uibk.ac.at

CONAN

CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes. Moreover, CONAN assists the evaluation process by visualizing detected associations via Manhattan plots in order to enable a rapid identification of genome-wide significant CNV regions. Various file formats including the information on CNVs in population samples are supported as input data. 
http://genepi-conan.i-med.ac.at/

Team

Publications

2011

Bib

Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht and Anita Kloss-Brandstätter: A Feedback Guided Interface for Elastic Computing. In Proceedings of the 23rd GI-Workshop Grundlagen von Datenbanken (GvDB 2011), Obergurgl, Austria, pages 109-114. 2011

Bib Link

Anita Kloss-Brandstätter, Dominic Pacher, Sebastian Schönherr, Hansi Weißensteiner, Robert Binna, Günther Specht and Florian Kronenberg: HaploGrep: A Fast and Reliable Algorithm for Automatic Classification of Mitochondrial DNA Haplogroups. In Human Mutation, vol. 32, no. 1, pages 25-32. Wiley Inc., 2011

2010

Bib Link

Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg and Anita Kloss-Brandstätter: CONAN: Copy Number Variation Analysis Software for Genome-wide Association Studies. In BMC Bioinformatics, vol. 11, no. 1, pages 318. 2010

Bib Link

Michael Borovicka, L. Laschitz, D. Reiter, E. Gächter and Günther Specht: Chaos or Content: Towards Generic Structuring of Medical Documents by Utilisation of Archetype-Classes. In eHealth Informatics meets eHealth 2010

Bib Link

Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg and Anita Brandstätter: eCOMPAGT integrates mtDNA: Import, Validation and Export of Mitochondrial DNA Profiles for Population Genetics, Tumour Dynamics and Genotype-Phenotype Association Studies. In BMC Bioinformatics, vol. 11, no. 1, pages 122. 2010

2009

Bib Link

Sebastian Schönherr, Hansi Weißensteiner, Stefan Coassin, Günther Specht, Florian Kronenberg and Anita Brandstätter: eCOMPAGT - efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology. In BMC Bioinformatics, vol. 10, no. 1, pages 139. 2009

1996

M. Holzner, M. Adler, M. Fischer, Günther Specht: Graphische Darstellung von Differentialdiagnosen in einem Begriffsnetz unter Verwendung von Snomed-kodierten Hypothesen, In Proceedings of the 41. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS '96), 15.-19.9.96 in Bonn

1995

Bib

Günther Specht and Martin Bauer: MultiMED-ein Multimedia-Datenbanksystem zur Aus-und Weiterbildung in der Röntgendiagnostik in der Orthopädie. In Hypermedia in der Aus-und Weiterbildung, Schriften zur Informationswissenschaft, vol. 17, pages 209-210. 1995