Department: Single-cell Open Lab (scOpenLab)
Code number: 2021-0378
The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.
A position as bioinformatician for implementing a multi-module data infrastructure that links imaging and genomics data is available at the DKFZ. These activities are embedded in a larger initiative for bioimage data management that aims at participation in the national infrastructure for research data management (NFDI). The goals of this initiative (NFDI4BIOIMAGE https://nfdi4bioimage.de/en/start/ ) are to provide solutions for the FAIR management of bioimage data, including standards for data file formats, tools for multimodal data integration, bioimage data analysis workflows and advanced training.
We are looking for a bioinformatician or computational biologist to implement and maintain workflows for the integrated analysis and mining of bioimaging and sequencing data. The position will involve:
- establishing an OMERO instance for standardized data management, metadata annotation
- develop a framework that utilizes (containerized) software for benchmarking / QC assessment
- linking the image database to omics data allowing researchers to cross-reference and annotate both image- and sequencing based datasets.
The successful candidate will be part of an interdisciplinary research and data management team developing and applying a diverse range of state-of-the-art methodology to implement and maintain data management and bioinformatics workflows. The role will involve close cooperation with other partners of the NFDI4BIOIMAGE initiative.
The project is coordinated by Prof. Elisa May, Dr. Jan-Philipp Mallm and Dr. Ivo Buchhalter at the DKFZ.
- Implementing an OMERO platform at DKFZ
- Extending the power of OMERO with automated data annotation tools and linked results / features
- Integration of OMERO with existing genomics data management platforms
- Testing / benchmarking workflows with cloud deployments and fast I/O strategies
- Implementing and monitoring a standardized pipeline management framework
- Developing a metadata database for sample/data tracking
We offer you the opportunity to help excel the scientific data infrastructures for the storage and exchange of bioimage data in Germany.
- Master's degree or equivalent qualification in bioinformatics, computational biology, computer science, statistics, mathematics, or similar background with experience in computational biology / bioinformatics of at least 2 years
- Proficiency with UNIX-based systems and relevant programming languages such as Python is a prerequisite
- Previous experience with OMERO / OME or other image management tools is highly welcome
- Software engineering skills to develop APIs for (meta)-data access are a plus
- Previous experience in complex data management, cloud computing, container technologies and system administration is beneficial
The ideal applicant should have demonstrated the ability to work independently and creatively. The candidate should have excellent communications skills and be able to articulate clearly the technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.
- Interesting, versatile workplace
- International, attractive working environment
- Campus with modern state-of-the-art infrastructure
- Salary according to TV-L including social benefits
- Possibility to work part-time
- Flexible working hours
- Comprehensive further training program
Earliest Possible Start Date: as soon as possible
Duration: The position is initially limited to 1 year. An extension up to 5 years is possible.
The position can in principle be part-time.
Application Deadline: 15.12.2021
Dr. Jan-Philipp Mallm
Phone +49 (0)6221/54-51378
Please note that we do not accept applications submitted via email.