Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

Energy-Aware Optimization of Bioinformatics Workflows

The research group for „Knowledge Management in Bioinformatics“ at the Institute for Computer Science, Humboldt-Universität zu Berlin, has an open research position in the area of energy-aware optimization of workflows for Bioinformatics data analysis. The position is paid according to TVL-E13 (roughly 4,200 – 4,600 Euro before tax, depending on prior experiences). It is open from the earliest possible start date on and will be funded until 30.6.2028. Our prime interest is to find a highly motivated PhD student, but applications from PostDocs are also eligible.


The position is part of the DFG-funded Collaborative Research Center FONDA – Foundations of Workflows for Large-Scale Scientific Data Analysis. In this project, more than 50 researchers jointly research innovative infrastructures for the large-scale analysis of scientific data sets. The CRC is highly interdisciplinary, embracing especially software engineering, distributed systems, algorithm engineering, data science, databases, bioinformatics, biomedical image analysis, material science, and satellite-based remote sensing. It centers on the concept of data analysis workflows (DAW), and aims to research new approaches to enhance human productivity in building and maintaining DAWs by developing new languages, optimization techniques, analysis algorithms, workflow compilers, network methods, and distributed resource management systems.

FONDA is a joint project of all Berlin universities and various other research institutions. FONDA will be funded for four years, with the possibility of further extensions. It is situated in Berlin, the capital of Germany. Over the last years, Berlin has developed into an international highly attractive city, both for working and living, with a very rich and intertwined network of high profile research organizations and universities.

The position

The position is part of FONDA subproject A2, which will employ two researchers, one supervised by Prof. Ulf Leser and one by Prof. Knut Reinert, Freie Universität Berlin, who will jointly study the problems of energy-aware workflow optimization and rewriting in Bioinformatics. We will develop methods to profile and monitor the energy consumption and CO2-production of Bioinformatics tools and workflows and develop new approaches to reduce energy consumption by workflow rewriting and workflow scheduling. Within this scope, the holder of this position will focus on designing energy forecasting and workflow optimization. There are no teaching duties.

The group

The holders of this position will work in an interdisciplinary team from computer science, medical informatics, and bioinformatics consisting of app. 10 full-time researchers plus students. We are engaged in a number of collaborative projects related to large-scale scientific data analysis, biomedical text mining, and translational bioinformatics. The group is, for instance, part of the DFG-funded Research Unit Beyond the Exome on the analysis of variants in non-coding genomic regions, and the Research Training Group CompCancer on computational methods in cancer research. The group is led by Ulf Leser, who is also speaker of the CRC FONDA.

Further information on the group may be found here.


  • (Very) good Diploma or Master in Computer Science or Bioinformatics, or equivalent qualification
  • Good knowledge in at least one of the following areas: Distributed system, energy-efficient systems, workflow systems, workflow / query optimization
  • Prior knowledge in and experiences with real-life Bioinformatics workflows is an advantage but not required.
  • Experience in programming, preferably in teams and in a research-oriented context
  • Ambition to pursue high-profile research and in pursuing a PhD (if applicable)
  • Strong interest in interdisciplinary research
  • Fluent English, very good communication skills


Please send your application by email to Prof. Leser. Please also send all questions directly to him. Applications will be screened as soon as they arrive. Late running applications might excluded from consideration.

Humboldt-Universität is an equal-opportunity employer. Applications from disabled persons are, if equally qualified, handled with preference. We strongly encourage applications by females. We strive for diversity.

Legal notice

This text is an informal description of the open position. The official announcement (only in German) can be found here.