➔ Poster (doi:
10.7490/f1000research.1114422.1)
AuthorsAarif Mohamed Nazeer Batcha 1*, Guokun Zhang 1*, Ulrich Mansmann 1
1 :
Department of Medical Informatics, Biometry and Epidemiology, University of Munich (IBE, LMU), Marchioninistrasse 15, 81377 Munich - Germany
* : Corresponding author
Abstract
The NGS-Fablab, an IT infrastructure for handling Next-Generation Sequencing data, was built for researchers at the university hospital and medical faculty of University of Munich. As one of the core modules of NGS-Fablab, Galaxy (version 2015) was deployed to provide bioinformatics platform for biomedical research projects in many different fields, including variant calling procedure, differential gene expression and copy number analyses. Since various types of NGS data could be provided from different locations, it was noticed that the data library inside of Galaxy is short of the strength to manage the metadata in an effective manner. To solve that issue, the Open Source Biology Information System (openBIS) was introduced into NGS-Fablab which has strong ability to track, annotate and share data throughout distributed research projects in the biological sciences. A direct connection between Galaxy and openBIS is till now not available. We have integrated openBIS into Galaxy by using Web2py (a python based webserver frame) so that a smooth communication between two systems is built. In our poster, we aim to elaborate the technical issues regarding building connection between Galaxy and openBIS, the functionality such as querying the metadata, running Galaxy workflow and updating downstream data afterwards. The potential further development will also be discussed, such as graphically summarizing the metadata and visualizing the down streaming analysis.
