Abstract
Over the last decade, advances in high-throughput technologies have resulted in a flood of new biological data. Here, individual samples can extend up into terabyte size. While potential applications are broad, ranging from biotechnology to medical applications, the analysis of these datasets poses massive challenges. In order to make use of the produced terabytes of data, these datasets need to be integrated, need to be mapped onto existing biological knowledge, and need to be explored by experts.
We present UniPAX and BiNA, a scalable system for the integration and analysis of high-throughput data (genomics, transcriptomics, proteomics, and metabolomics) in a network context. A central data warehouse holds the core dataset. A flexible middleware can execute custom queries on this dataset and communicate with our visual analytics tool BiNA, the Biological Network Analyzer. We demonstrate how the combination of these tools permits an efficient analysis of large-scale datasets for medical applications.
About the authors
Andreas Gerasch studied Bioinformatics at the University of Tübingen and is currently writing his doctoral thesis on biological network visualization and analysis. He mostly worked on graph algorithms and layout, visualization techniques, data integration methods, combinatorial problems, and omics data.
Universität Tübingen, Dept. for Computer Science, Sand 13, D-72076 Tübingen
Jan Küntzer is a senior scientist medical informatics in Pharma Research at Roche Diagnostics GmbH. With a background in computer science and mathematics, he did his Ph.D. at Saarland University in Bioinformatics with a primary focus on Integrative Systems Biology. During his research he spent a year at Leeds University in the UK and did a research fellowship at Kyoto University in Japan. Dr. Küntzer joined Roche 2008 with a Roche Postdoc Fellowship working on a biological information system for cancer genome mutation data that integrates publicly available data with in-house data. Since 2010 he is working as a senior scientist medical informatics on global research projects with a focus on systems development and the analysis of biological networks
Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Nonnenwald 2, D-82377 Penzberg, Germany
Peter Niermann studied Bioinformatics at the University of Tübingen and is currently writing his doctoral thesis on computational analysis of metabolic networks. He focuses on the integration and analysis of omics data.
Center for Bioinformatics, Universität Tübingen, Sand 14, D-72076 Tübingen
Daniel Stöckel studied Bioinformatics at the Center for Bioinformatics at Saarland University where he is currently writing his doctoral thesis. His interests lie in biological network inference and the detection of deregulated subgraphs and gene sets.
Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany
Michael Kaufmann is head of the algorithms group at the department of computer science at the University of Tübingen. He mostly works on graph algorithms, combinatorial problems with geometric flavour and visualization of networks in various applications.
Universität Tübingen, Dept. for Computer Science, Sand 13, D-72076 Tübingen
Oliver Kohlbacher studied chemistry and computer science at Saarland University, Saarbrücken. After obtaining his Diplom (Chemistry, 1996) and his PhD (Computer Science, 2001) he became a group leader at the Center for Bioinformatics Saar and spent two years at Celera Genomics, Rockville, MD, USA as a Postdoc. Since 2003 he has been a full professor for Simulation of Biological Systems (2003–2011) and Applied Bioinformatics (2011–) at University of Tübingen. In 2012 he founded the Quantitative Biology Center (QBiC) at University of Tübingen. Since 2013 he has been an adjunct professor of the faculty of medicine at University of Tübingen.
Center for Bioinformatics, Universität Tübingen, Sand 14, D-72076 Tübingen
Hans-Peter Lenhof studied Mathematics (Diplom 1989) and Computer Science (Promotion 1993, Habilitation 1999) at Saarland University. Since 2000 he is a full professor for Bioinformatics at the Center of Bioinformatics of Saarland University
Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany
©2015 Walter de Gruyter Berlin/Boston
