Health Data


Health Data


Health Data Overview


The Health Data Hub focusses on processes in medical informatics and bioinformatics with the aim of automatisation and bringing new research results faster into healthcare. A fundamental challenge of a digital healthcare environment is the growing amount of sensitive patient data, e.g. created by smart wearables or whole genome analyses. Handling and processing of such huge data sets in daily routine diagnostics requires new infrastructures and IT solutions. Therefore, large-scale IT and cloud solutions are also a responsibility of the Health Data Hub. The Health Data division in Berlin is subdivided in three groups:  Cloud  & IT, Medical Informatics and Datamanagement.


One Touch Pipeline

One Touch Pipeline (OTP) is an automation platform for processing next generation sequencing (NGS) data. The application provides support in all steps of this process, including data registration, storage handling, quality monitoring, alignment of reads to reference genomes and all crucial types of variant calling. OTP has been developed since 2013 and is used for all genomic projects of HiDiH in Berlin and Heidelberg. The data collection in Heidelberg comprises about 50.000 samples and a data storage volume of more than 10 petabytes. The OTP roll out for Berlin is in the ramp up phase.


From software architecture perspective, OTP is both information center and workflow system. Meta-data files describing sequences are uploaded into the database, involving curating steps and manual interventions in case of ambiguities. Based on complete and consistent information, data management and bioinformatics workflows are executed with all steps book-kept in a database. CPU and I/O intensive jobs are sent to our high performance computing clusters.

The application provides three major benefits to stakeholders: first, the automation process reduces the man-power required for data management. Second, all operations are executed more reliably and faster reducing the time until the sequences can be analysed by bio-informatics groups. Third, all information is located in one system with secure web access and search capabilities.

The application was implemented using Grails framework in Groovy programming language with web layer in HTML5. The Grails framework provides support for dependency injection from Spring framework and object relational mapping using Hibernate. The authorisation is programmed using Spring Security annotations with authentication based on LDAP system. The application is deployed on Apache Tomcat web container and PostgreSQL is used as a database engine. The application is managing data and processes in two separate computing realms with petabyte scale file system and computing cluster operated by job schedulers as SLURM and PBS in each realm.

External German projects are supported in the context of the Heidelberg Center for Human Bioinformatics as part of the German Network for Bioinformatics Infrastructure (de.NBI) supports OTP for de.NBI users. Among others, these are the Heidelberger Center for Personalized Oncology (DKFZ-HIPO), the German Consortium for Translational Cancer Research (DKTK) and the Berlin program Precisioned Digital Oncology (PeDiOn).

Medical Informatics Initiative - HiGHmed

The Health Data Hub supports the use cases oncology and cardiology within the HiGHmed consortium

The oncology use case deals with the challenge of integrating enormous amounts of data from genome sequencing and radiology into clinical practice. The possible treatment of cancer patients is discussed in virtual molecular tumor boards and the expertise of various institutions such as doctors, researchers and patients is brought together. The aim is to better identify similar cancer cases and enable individual patient-oriented treatment. To this end, the Health Data Hub is setting up a data integration center for OMICS data (omicsDIC). It automates the processes for processing and analyzing sequencing data using the One Touch Pipeline (OTP) software.

In the fields of cardiology and pneumology, the main focus is on the comprehensive collection of disease, treatment and health data, with particular emphasis on compliance with medical informatics standards. For the most holistic view possible, not only the data from the practice and clinic are taken into account, but also PREMs, PROMS and vital data that patients collect in their home environment.


Groups Berlin

Cloud & IT

Harald Wagener2

Harald Wagener worked in the IT industry for 20 years, building and operating large scale and distributed Cloud infrastructures. In 2020, Harald Wagener joined the "Health Data" research group as Group Leader Cloud for the Cloud team in Berlin. His focus is on the Berlin node of de.NBI Cloud and European Life Science Cloud efforts.

Harald Wagener

Group leader Cloud & IT

BIH@Charité - Center of Digital Health
Kapelle-Ufer 2
10117 Berlin

Research Group Cloud & IT

Martin Braun
Cloud Developer
Max Boshof
Trainee System-Integration
Christian Buggedei
Business Owner Health-X dataLOFT
Jakob Mathis
Sytems Administrator IT
Stefan Schneider
IT-System Administrator Cloud
Foo Wei Ten
IT-System Administrator Cloud

Medical Informatics

Dirk Meyer zum Büschenfelde is a clinical chemist and business informatics specialist with more than 10 years of experience in the field of laboratory medicine. His work marks the interface between healthcare and technology, using data to continuously improve outcomes and processes. Since 2022, his main focus has been on the comprehensive collection of disease, treatment and health data, with a particular emphasis on compliance with medical informatics standards.

Dr. Dirk Meyer zum Büschenfelde

Group leader Medical Informatics

BIH@Charité - Center of Digital Health
Kapelle-Ufer 2
10117 Berlin

Research Group Medical Informatics

Severin Kohler
Medical Informatician
Dr. Maximilian Meixner
Medical Informatics Scientist


Sven Twardziok has 15 years of experience in the management and processing of large biological datasets, gained in various institutes as well as in industry. His work focusses on the development of data infrastructures to make data available to researchers according to the FAIR principles (Findable, Accessible, Interoperable, Reusable). He is actively involved in several initiatives such as de.NBI, ELIXIR, DZPG, DZKJ, NCT and MII.

Dr. Sven Olaf Twardziok

Group leader Datamanagement

BIH@Charité - Center of Digital Health
Kapelle-Ufer 2
10117 Berlin

Research Group Datamanagement

Dr. Marcel Jentsch
Data Manager
Tauseef Naumann
Cloud Manager
Dr. Valentin Schneider-Lunitz
Philipp Strubel
Software Developer
Alma Runde
Ulrike Taron
Data Manager

Groups Heidelberg

Health Data Science Unit

Jürgen Eils headed the “Data Management and Genomics IT” at the German Cancer Research Institute for 15 years. Since 2018 Jürgen Eils jointly lead the "Health Data" research group within HiDiH with teams both in Berlin and Heidelberg. His work focusses on Big Data research and services in the fields of genomics and health.

Jürgen Eils

Group leader at Health Data Science Unit (HDSU), Medical Faculty Heidelberg

Medical Faculty Heidelberg

BioQuant-Zentrum BQ054

Im Neuenheimer Feld 267
69120 Heidelberg

Research Group Health Data Science Unit


ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer Analysis of Whole Genomes, Nature, 578(7793), 82-93, doi: 10.1038/s41586-020-1969-6


Yakneen, S.§, Waszak, S.M., PCAWG Technical Working Group, Gertz, M., Korbel, J. O.§, PCAWG Consortium (2020). Bulter enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, Epub ahead of print, doi: 10.1038/s41587-019-0360-3


Ishaque, N.*, Abba, M.L.*, Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Kleinheinz, K., Toprak, U.H., Hutter, B., Benner, A., Shavinskaya, A., Zhou, C., Gu, Z., Kerssemakers, J., Marx, A., Moniuszko, M., Kozlowski, M., Reszec, J., Niklinski, J., Eils, J., Schlesner, M., Eils, R., Brors, B. & Allgayer, H.§ (2018). Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature Communications, 9(1), 4782. doi: 10.1038/s41467-018-07041-z


Gröbner, S.N.*, Worst, B.C.*, Weischenfeldt, J., Buchhalter, I., Kleinheinz, K., Rudneva, V.A., Johann, P.D., Balasubramanian, G.P., Segura-Wang, M., Brabetz, S., Bender, S., Hutter, B., Sturm, D., Pfaff, E., Hubschmann, D., Zipprich, G., Heinold, M., Eils, J., Lawerenz, C., Erkek, S., Lambo, S., Waszak, S., Blattmann, C., Borkhardt, A., Kuhlen, M., Eggert, A., Fulda, S., Gessler, M., Wegert, J., Kappler, R., Baumhoer, D., Burdach, S., Kirschner-Schwabe, R., Kontny, U., Kulozik, A.E., Lohmann, D., Hettmer, S., Eckert, C., Bielack, S., Nathrath, M., Niemeyer, C., Richter, G.H., Schulte, J., Siebert, R., Westermann, F., Molenaar, J.J., Vassal, G., Witt, H., Burkhardt, B., Kratz, C.P., Witt, O., van Tilburg, C.M., Kramm, C.M., Fleischhack, G., Dirksen, U., Rutkowski, S., Fruhwald, M., von Hoff, K., Wolf, S., Klingebiel, T., Koscielniak, E., Landgraf, P., Koster, J., Resnick, A.C., Zhang, J., Liu, Y., Zhou, X., Waanders, A.J., Zwijnenburg, D.A., Raman, P., Brors, B., Weber, U.D., Northcott, P.A., Pajtler, K.W., Kool, M., Piro, R.M., Korbel, J.O., Schlesner, M., Eils, R., Jones, D.T.W., Lichter, P., Chavez, L.§, Zapatka, M.§, Pfister, S.M.§ (2018). The landscape of genomic alterations across childhood cancers. Nature, 559(7714), 321-327, doi: 10.1038/s41586-018-0167-2


Reisinger, E.§, Genthner, L., Kerssemakers, J., Kensche, P., Borufka, S., Jugold, A., Kling, A., Prinz, M., Scholz, I., Zipprich, G., Eils, R., Lawerenz, C., Eils, J. (2017). OTP: An automatized system for managing and processing NGS data. Journal of Biotechnology, 10(261), 53-62, doi: 10.1016/j.jbiotec.2017.08.006


*these authors contributed equally

§corresponding author

Latest News

SBHD 2024

Our colleaugues at Vanderbilt University organise the 16th INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY OF HUMAN DISEASE – SBHD 2024 this year from June 10-12. Don’t miss the opportunity to

Top 100 Köpfe der Wissenschaft 2023

Am 11.10.2023 wurde Prof. Roland Eils im Tagesspiegel als einer der 100 wichtigsten Köpfe der Hauptstadt-Wissenschaft gewürdigt. So schreibt der Tagesspiegel: "Um Big Data dreht sich alles in der

Young BIH scientists attend 72nd Lindau Nobel Laureate Meeting

The Lindau Nobel Laureate Meetings are annual conferences where some of the brightest minds in science converge to exchange knowledge, foster collaboration, and inspire the next generation of

Roland Eils wird als Highly Cited Researcher international gelistet.

Roland Eils gehört zu den weltweit am häufigsten zitierten Forschenden des Jahres 2022, wie aus der Liste der „Highly Cited Researchers“ hervorgeht, die das Unternehmen Clarivate heute veröffentlicht