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 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.
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.
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.