Data Management and IT Infrastructure
Maintaining state-of-the-art technology platforms for medical research is meanwhile imperatively connected to highly capable IT infrastructure. Exponential growth of multi-omics research data, a plethora of clinical data types as well as privacy protection guidelines make data storage and management a challenging duty. The IKMB provides a huge portfolio of compute and storage facilities to its users and partners. A high-performance compute cluster with over 1000 CPU cores, storage infrastructure encompassing over 2PB of hard disk and an encrypted cloud archive, as well as several stand-alone high-performance compute systems (GPU, FPGA, high RAM) are at our scientist’s disposal.
Current efforts also include the faculty-wide implementation of several data management appliances using YODA (Your Data) an iRODS-based data management infrastructure, developed at Utrecht University. For several clinical projects we currently enroll REDcap database systems, developed at Vanderbilt University, to store survey data and other clinical data, such as clinical parameters, diagnoses and medication. To facilitate the distribution of massive OMICs data collections, we plan to implement a new storage resource connected to the Globus Connect Network maintained by University of Chicago. And as part of the German Human Genome Phenome Archive (GHGA), we are currently working on the integration of our data infrastructure with the GHGA network.
We will bundle the current developments for data management and bioinformatics web services in a Genomics Data Integration Centre (GenDIC). The GenDIC currently comprises the following components:
| • Yoda research data management (RDM) service | https://yoda.i-kmb.de/ |
| • Yoda research data management (RDM) service for the DFG Research Unit (RU) miTarget | https://yoda-mitarget.medfdm.uni-kiel.de/ |
| • Jupyterhub bioinformatics e-learning software environment at IKMB | https://jupyter.ikmb.uni-kiel.de |
| • Hybrid computing webservices: GDPR-compliant bioinformatics web services with FPGA/GPU support | https://hybridcomputing.ikmb.uni-kiel.de |
| • RedCap system for clinical and translational research databases | https://redcap.ikmb.uni-kiel.de/ |
Contact:
Georg Hemmrich-Stanisak
David Ellinghaus
IKMB Laboratory Information and Management System (LIMS)
Our LIMS (Laboratory Information and Management System) is developed in-house and consists of a relational database (Microsoft SQL Server 2019) including graphical user interfaces. It plays an important role in quality control and lab automation by facilitating lab processes for technical staff and enabling scientists to perform targeted data analyses. It is used for managing blood and DNA samples, proband, family and phenotype information as well as genetic markers and assays (TaqMan, Sequenom, Illumina). Genotypes can be imported and data for genetic analysis exported. All tools are written in Visual Basic (version 2010).
Contact: Lars Kraemer