Position: Bioinformatician / Workflow Developer
Department: German Human Genome-Phenome Archive (GHGA)
Code number: 2021-0405
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.
The German Cancer Research Center is seeking for the recently launched infrastructure initiative German Human Genome-Phenome Archive a bioinformatician / workflow developer.
The German Human Genome-Phenome Archive (GHGA, www.ghga.de) is part of the national program for research data infrastructures (NFDI). As part of the federated European Genome-Phenome Archive, GHGA will contribute towards the establishment of an international infrastructure for human genome data. These activities are closely coordinated with leading international initiatives and networks, such as the Global Alliance for Genomics and Health (GA4GH). This infrastructure will support genomics data hubs with software tools for secure data / metadata storage, interactive data portals with data visualization, and streamlined data deposition and acquisition solutions. The GHGA main office, which is coordinated by Prof. Oliver Stegle (Division of Computational Genomics and Systems Genetics), is located at DKFZ in close coordination with the European Molecular Biology Laboratory (EMBL, Prof. Jan Korbel).
We are looking for a bioinformatician or computational biologist to implement and maintain data processing and analysis workflows as part of GHGA. The job will involve implementing and optimizing existing standardized data processing frameworks that utilize workflow languages (in particular NextFlow) and containerized software. The applications will range from basic data QC and processing to complex variant calling workflows and data integration methods. 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 bioinformatics workflows in a cloud compute environment. The role will involve close cooperation with other partners in the GHGA network, as well as international networks and initiatives.
- Implementing and monitoring a standardized pipeline management framework on cloud environment
- Workflow development and maintenance for NGS data processing and analysis including:
- Somatic and germline variant calling (SNV, Indel, SV, CNV, …)
- Data integration and visualization
- Containerization of existing workflows
- Improvement of bioinformatics workflows with respect to performance and stability
- Testing / benchmarking workflows with cloud deployments
- Development of cloud images for (human) bioinformatics
We offer the opportunity to help shape one of the most important emerging scientific data infrastructures for the storage and exchange of omics data in Germany.
- Get exposed to a plethora of fields ranging from AI-guided clinical decision making to modern web development technologies
- Work with an interdisciplinary team of experts bringing state-of-the-art biomedical research closer to clinics and patients
- Take part in international organizations such as the Global Alliance for Genomics and Health (GA4GH), the European Genome-phenome Archive (EGA) and ELIXIR shaping the future of genomics across borders
- Widen your expertise with extensive possibilities of training programs, seminars and conferences
- PhD in computer science, mathematics, physics, bioinformatics, computational biology or similar background with focus on bioinformatics or data science; alternatively a MSc or equivalent qualification with complementary years of relevant experience
- Hands-on experience with workflow development and genomics data analysis using open source software and algorithms, using workflow languages (WDL, CWL, Nextflow)
- >2 years of experience with software containerization tools like Docker, Singularity
- Proficiency with UNIX-based systems and relevant programming languages such as Python or R is a prerequisite
- Expertise in software development and cloud computing 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 2 years with the possibility of prolongation.
The position can in principle be part-time.
Application Deadline: 28.01.2022
Dr. Koray Kirli
Phone +49 (0)6221/42-3473
Please note that we do not accept applications submitted via email.