Job: Oncology Bioinformatics - System Administrator Clinical Genomics Platform (m/f), Darmstadt, Germany
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2.9 years ago by
gap.rattimasakol20 wrote:

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
rna-seq job alignment assembly • 1.3k views
ADD COMMENTlink modified 2.9 years ago by schelhorn50 • written 2.9 years ago by gap.rattimasakol20

Curious? Apply and find more information at

ADD REPLYlink written 2.9 years ago by gap.rattimasakol20

Please share the link to so that everyone can be directed to original job posting in the merck website? I think in that way it will be better for people to apply.

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.8k

And in which country?

ADD REPLYlink written 2.9 years ago by Daniel3.7k
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2.9 years ago by
schelhorn50 wrote:

I believe I can chime in here to answer some of the questions; I am a member of the Bioinformatics team that is hiring for this position. The role is one of several positions we are currently filling in the Global Early Development/Oncology Bioinformatics section of the Merck Biopharma business. The unit is located in Darmstadt, Germany, 30m train ride from Frankfurt or Mainz, both of which are attractive places to live as well.

The position is geared towards advanced analyses of large genomics (and in the futire also imaging, mobile sensor etc.) data for clinical projects; in particular we are looking for a bioinformatics HPC administrator who maintains our new GxP-validated clinical genomics analysis platform. All newly hired roles will work closely with me on this platform, and will have a very visible impact in the organization (and freedom to shape future decisions) by transforming it into a more comprehensive solution that implements the clinical precision medicine strategy for the whole company. This position is definitly for someone who likes to shape future decisions, is eager to constantly learn new technical and scientific skills, and communicate a lot with our team of bioinformatics experts and related functions. Applications also from academia postdocs, related areas of scientific computing and other fields of bioinformatics are encouraged – motivation to learn, diligence, a good understanding of genomics, and interest in HPC are of primary importance. You will more have more than enough interesting problems to work on to keep you stimulated.

In my view, we are lucky to have very friendly and focused team here; the company is in good shape, and bioinformatics in particular is taking on a lot of interesting projects at the moment. Besides the usual (rather terrific, in my opinion) financial benefits of a permanent position in biopharma, the company can offer industry-leading vacations times (42 days annually, in addition to 10 German public holidays), and a very liberal (and family-friendly) work-at-home policy. As I mentioned before, commuting from Frankfurt or Mainz to Darmstadt is possible within 30m by public transport, and the environment is surrounded by large forests that make for great hikes. Public healthcare, public transport, and childcare support are all good as well. In my personal experience, there are only a handfull of bioinformatics positions each year in Germany that are as attractive as this offer. So apply and let's have a chat!

Direct link:

Oncology Bioinformatics - System Administrator Clinical Genomics Platform (m/f) (148337)

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by schelhorn50
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