Bioinformatics Software Engineer

European Molecular Biology Laboratory

Germany

November 19, 2021

Description

Bioinformatics Software Engineer Location: Heidelberg, Germany

Staff Category: Staff Member Contract Duration: 3 years Grading: 4 or 5, depending on individual qualifications and experience Closing Date: 19 November 2021 Reference Number: HD02063

The Bork group is seeking a highly motivated bioinformatics software engineer to collaboratively design, build, and run data analysis workflows for microbiological research both for scientists within the lab and for researchers across Germany, via the group's membership in the National Research Data Infrastructure consortium “NFDI4Microbiota.”

Your role

In this role you will work closely with researchers within the Bork group and software engineers across the consortium to design, develop, run and maintain bioinformatic software and databases and combine them into advanced workflows. You will also contribute to the design and development of web front-ends and APIs, backed by cloud infrastructure. The systems you design and build will be part of a new core national infrastructure which will support the research of microbiologists across Germany. The position also involves large-scale data handling (e.g. of next-generation sequencing data) and executing and monitoring data analysis pipelines.

You have
  • Experience designing and developing web interfaces and databases
  • Experience in cloud computing infrastructure and tools to manage research analysis pipelines (e.g. Common Workflow Language, NextFlow, Snakemake)
  • Experience in Python, especially with web frameworks such as flask or fastapi
  • Willingness to learn new skills as projects require
  • Good communication, interpersonal and English language skills
  • Appreciation for open science and data sharing to facilitate scientific research
  • Ability to work both independently and in a team
  • You might also have
  • Familiarity with user-centric design and testing
  • Experience with testing and CI/CD knowledge would be helpful.
  • Knowledge of deployment with via Docker + Kubernetes
  • Experience writing training materials and/or documentation
  • Experience working at the interface between biology and computation
  • Experience in data analysis, statistics and visualisation, e.g. in Python or R
  • Experience with compute clusters (e.g. SGE, slurm)
  • Familiarity with processing next-generation sequencing or other large- scale microbiomics data
  • A Master's or PhD degree in Bioinformatics, Computer Science, Computational Biology, or related fields
  • Why join us

    EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus.

    What else you need to know

    We are Europe's flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with approximately 2000 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

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