Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Research Projects

Image: Structured Analysis and Integration of RNA-Seq Experiments - de.STAIR

Structured Analysis and Integration of RNA-Seq Experiments - de.STAIR

RNA sequencing (RNA-Seq) has become a widely used tool to study quantitative and qualitative aspects of the transcriptome. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. Our aim is to enable a comprehensive analysis of RNA-Seq experiments as a service. To enable maximum usefulness, interconnectivity, and accessibility for the developed approaches and services, we will provide dedicated workshops, training programs and screen casts for bioinformaticians and other life scientists and, ultimately, lower the barriers to RNA-Seq data analysis as a whole.

To contribute towards facilitating "The German Network for Bioinformatics Infrastructure", we want to i) establish flexible workflows for RNA-Seq protocols and experimental designs as a service, ii) embed the RNA-Seq data into an advanced biological context by integrating other data sources and experiments and iii) develop, adjust and accommodate novel analysis methods with the RNA Bioinformatics Center (RBC) workbench. The new workflows and tools will become integral parts of RBC’s GALAXY platform and server infrastructure. The integration into GALAXY assures the portability of tools, workflows and pipelines to other hardware infrastructures. The partner project de.STAIR will participate in the RBC trainee program aiming at interested bioinformaticians from other sites to give specialised trainings for advanced RNA-Seq analysis. In addition, de.STAIR will also offer iv) courses for specialists and webinars for scientists and students without a background in bioinformatics. These training courses will cover aspects of the experimental design of RNA-Seq studies, beginners’ introduction to use the GALAXY workflows and data integration tools. On-site workshops will familiarize bioinformaticians as well as trained experimentalist with the de.STAIR workflows and the advanced computational biology of regulatory RNAs.

Research Team

de.NBI
German Network for Bioinformatics Infrastructure
Dr. Dr. Steve Hoffmann
Interdisciplinary Center for Bioinformatics
University of Leipzig,
Leipzig, Germany
Prof. Dr. Wolfgang Hess
Dept. for Biology III
Albert-Ludwigs-University Freiburg,
Freiburg, Germany
RNA Bioinformatics Center - RBC
Federal Ministry for Education and Research (BMBF)
Projektträger Jülich