Your role: We are currently setting up a GxP validated clinical genomics platform for analyzing next-generation sequencing (NGS) data of patients from clinical trials. The aim of this project is to enable routine use of various NGS approaches in the framework of clinical studies at Merck. The role of the “System Administrator Clinical Genomics Platform (m/f)” is to administer the underlying high-performance computing (HPC) Linux cluster, its resource manager, storage back-ends, and validated NGS analysis software applications. The position is embedded within a team of data analysis and NGS experts from research and bioinformatics. Besides maintaining the NGS analysis pipeline on an application level and providing user and storage management for the platform, the role also encompasses extending NGS analysis workflows together with our experts from bioinformatics as well as acting as the responsible validation owner of the overall GxP validated system and the associated processes and interfaces.
Who you are:
- Experience with administering and optimizing Linux HPC Linux compute cluster resources, the associated resource managers (eg, SLURM), and high-performance storage and database backends (eg, BeeGFS, iRODS, Oracle)
- Experience administering and running open-source and commercial parallel NGS pipelines (WES, WGS, WTS, deeply sequenced panels) implemented in Java, Shell, and Python in high-volume production environments
- Ability to script efficiently in shell and Python to automatize monitoring of processes and extend existing NGS pipelines with custom workflows
- Ability to work on patient data in a secured environment and experience in implementing technical security measures such as fine-grained access permissions and encryption protocols
- Ability to perform tasks in a timely, well-documented, highly conscientious, and responsible manner in order to keep the system in an audit-ready and compliant state
- Ability to communicate effectively and proactively with oncology bioinformatics, system infrastructure & operation team, the quality control and validation team, the clinical data management team