Data Engineer

Data Engineer


The University of Basel is the oldest university in Switzerland, it counts over 12'000 students and 4'300 researchers in 7 faculties active in domains from humanities, economy to natural sciences. In this context, sciCORE is the center of competence in scientific computing, maintaining an advanced computing infrastructure for active research and the associated services (including data management and scientific support). sciCORE is in particular developing and maintaining a secure IT infrastructure, sciCOREmed, suitable for biomedical research with data from hospitals. sciCOREmed is co-funded by the University of Basel and by the national project BioMedIT, managed by SIB - Swiss Institute of Bioinformatics, in support of the initiative Swiss Personalized Health Network (SPHN). In the current phase of implementation of BioMedIT services (2021-2024), Swiss university hospitals are ramping up the adoption of standardized data formats and exchange protocols to make patient data more easily available for research. We are seeking to reinforce our support capacity with such advanced data management technologies and concepts, bridging the gap between data managers in hospitals and data scientists in academia.
Our new collaborator will support projects making use of the national biomedical data infrastructure in support of research. The main focus of activity will be to support the data sharing goals of the "National Data Stream" project SwissPedHealth hosted at sciCOREmed which aims a making pediatric data collected in seven children hospitals (including the all university hospitals in Switzerland) seamlessly available for research. Simultaneously you will collaborate with other partners in the BioMedIT network to enable technical interoperability with other SPHN-funded projects and services. In practice the position will imply close contact with the projects' data managers and data scientists, to understand their needs at the technical level, to work out technical solutions and execute their implementation. The position will require flexibility and curiosity, a good sense of organization and a support-oriented mindset. You will be able to work with various data management tools and services (including semantic services), understand their APIs and develop scripts and automation to streamline data management processes in the projects.
As part of an agile and cooperative work environment you will be integrated in the local team of system, data management, and data analysis specialists at sciCORE, and work closely with data managers at other sites of the BioMedIT network (ETH, Uni Lausanne, and SIB) and with the semantic experts of the Personalized Health Informatics Group of SIB in Basel. The position is bound to the funding of BioMedIT project and is available immediately.
Duration of contract: two years with possibility of extension depending on availability of funds.

Your position

As our new collaborator, you will:

  • Develop a technical understanding of the data life cycle in the SwissPedHealth project (clinical data, genomics and other *omics data, ...)
  • Collaborate with data engineers, working groups and the data coordination center (DCC) in the SPHN initiative to identify reusable technologies and processes
  • Acquire practical know-how with the tools used in the BioMedIT network (data management systems, data transfer tools, semantic tools)
  • Develop, implement and maintain "glue software" and workflows between the tools and services used to integrate and share complex scientific data
  • Collaborate with the sciCORE scientific IT specialists to develop/adapt data management solutions
  • Provide support to data managers in using and adapting the project data environment (from API to GUI to data modeling)

Your profile


  • PhD or Masters with 3 or more years of work in academic research
  • Experience of work with scientific data management systems (e.g. LIMS, such as, LabKey, OpenBIS, ...), including work with APIs
  • Experience in programming with scripting languages (Python, javascript) in Linux environment
  • Understanding of databases (SQL, NoSQL, graph databases) and data modeling
  • Motivated by work in a support role in academic-research context
  • Proactive, service-oriented and collaborative spirit of mind
  • Fluent in English (oral and written) as working language


  • Experience in developing complex data-processing workflows
  • Experience with collaborative software development (git)
  • Experience with semantics technologies (RDF, GraphDB, SPARQL, biomedical ontologies)
  • Experience with interactive data-analysis environment (R/RStudio, JupyterLab)
  • Prior experience in support to biomedical research

We offer you

  • An opportunity to work in a project with a significant health and social impact
  • A friendly local and national network of domain-specialists
  • A chance to develop creative-yet-robust solutions to practical data management challenges
  • The opportunity to work with cutting-edge scientific computing and data management technologies
  • The social benefits of the University of Basel

The position is available immediately. The initial contract is for 2 two-year period with the possibility for extension on funding availability.


Application / Contact

If you are interested in this challenging and highly interesting position, please submit your application including CV, letter of motivation and references through our online portal. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered. For further information regarding the position, please contact


The position will remain open until filled. Start date is as soon as possible.

University of Basel

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Deadline: 2023-04-09
Location: Switzerland, Basel
Categories: Biomedical Sciences, Computer Engineering, Computer Sciences, Data management, Data Science, PhD, Programming, research data,


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