For better patient care: Cooperation between MIRACUM and the German Network for Bioinformatics Infrastructure (de.NBI)

The German Network for Bioinformatics Infrastructure, de.NBI in short, is a project funded by the BMBF for six years to design and implement a platform for high-quality and sustainably usable bioinformatics software and services. The network offers support and training for a broad spectrum of data analyses and bundles bioinformatics expertise in Germany. With the de.NBI Cloud and the Galaxy analysis platform, the de.NBI also makes IT infrastructure and storage capacities freely available to all scientists. Reproducible and trustworthy infrastructures are not only important for scientific research, they are essential for any medical application and patient care. One goal of the de.NBI network is therefore to certify the de.NBI Cloud established in the project, thus make it usable for sensitive data, and use cases in clinical practice, such as those promoted by the Medical Informatics Initiative.

The medical informatics initiative aims to create the conditions for closer collaboration between research and care. In the four-year project currently underway, all of Germany’s university hospitals are working together with research institutions, companies, health insurance companies and patient representatives to develop the framework conditions that will enable findings from research to reach patients directly. With ten university hospitals, the MIRACUM consortium (Medical Informatics in Research and Medicine) is the largest consortium and has three concrete use cases in which it addresses the optimization of patient recruitment, the development of machine learning methods, and the support of the molecular tumor board. The use cases show very well the numerous intersections between de.NBI and MIRACUM.

The MIRACUM use case From Knowledge to Action – Support for the Molecular Tumor Board, as one example, strives to identify potentially effective treatment options with targeted therapy for tumor patients after guideline-based treatment has been exhausted in the context of precision medicine. To this end, members of the MIRACUM project and de.NBI are working together to integrate analysis techniques into patient care in the form of bioinformatics workflows. In the MIRACUM use case, an analysis workflow, the MIRACUM Pipe, has already been developed for DNA sequencing that combines MIRACUM’s bioinformatics and clinical expertise. This is also available in the Galaxy version with the corresponding tools and frameworks from de.NBI. With such workflows, the high-throughput data measured in the laboratory can be processed in such a way that they can then be visualized in the translational research platform cBioPortal in an interactive PDF report and ultimately provide clinicians with decisive support in the preparation of a therapy recommendation. The Galaxy framework supported by de.NBI ensures high usability and reproducibility of the results.

de.NBI and the projects funded by the medical informatics initiative complement each other and build on each other in order to ensure a reliable and secure IT infrastructure between research and patient care in Germany.