About the position

A permanent position as senior engineer is vacant in the bioinformatics ELIXIR team, the position is externally funded. The position will be part of the Oslo bioinformatics ELIXIR team, which is the Oslo node of the ELIXIR Norway project. The Oslo bioinformatics ELIXIR team is part of the Centre for Bioinformatics hosted at the Department of Informatics (IFI) at the University of Oslo.

The ELIXIR Norway project is part of a European bioinformatics infrastructure program to ensure timely sustainable use of data and bioinformatics tools for life sciences. ELIXIR Norway is currently jointly funded by the Norwegian Research Council and the partner universities and organizations.

Project description

The position will be part of the ELIXIR development/operations team at the University of Oslo (UiO), participating in the development, implementation and operation of functionality for various national and international solutions provided by ELIXIR Norway, including:

• Nationally coordinated development and operations of the ELIXIR Norway infrastructure aimed at Norwegian researchers, which includes:
  • https://usegalaxy.no, a national web-based portal hosting Life Science-related tools and workflows provided by ELIXIR Norway with related cloud-based computational resources, including a pan-European job execution network. Usegalaxy.no is a national installation of an end-user framework called Galaxy (https://galaxyproject.org), which has a large international community of users and developers, especially within bioinformatics.
  • The National e-Infrastructure for Life Science (NeLS, https://nels.bioinfo.no), which provides storage resources for individual researchers and research projects, alongside related services, such as user/project management; features supporting ELIXIR help desk activities to researchers; data transfer to/from DNA sequencing facilities, analysis platforms and research data archives; and FAIR (https://www.go-fair.org/fair-principles/) solutions for research data management.
  • Computational tools and workflows related to High Throughput Sequencing (HTS) or Systems Biology, including writing wrapper scripts to allow embedding of existing tools into Galaxy
  • Base services supporting operation of other national and local ELIXIR Norway services, including user authentication/authorization and service operation monitoring.
• In addition, the University of Oslo node hosts a range of services that are part of the portfolio of functionality provided or facilitated by ELIXIR Norway:
  • The Norwegian Federated European EGA (European Genome-Phenome Archive) node (https://ega.elixir.no), which will store DNA sequences and other sensitive data deposited by Norwegian researchers within a highly secured infrastructure called Services for Sensitive Data (https://www.uio.no/english/services/it/research/sensitive-data/), while allowing sharing of metadata and data with installations of other EGA installations in Europe, within the bounds of GDPR, national laws and research ethics approvals.
  • The FAIRtracks software ecosystem (https://fairtracks.github.io) providing standards and services for annotating genomic and epigenomic datasets related to DNA positions (genomic track data) with FAIR metadata, including the TrackFind service (http://trackfind.elixir.no) for querying such metadata.
  • The Genomic HyperBrowser (https://hyperbrowser.uio.no), a python-based framework providing an advanced statistical analysis engine for genomic track data, libraries and file formats for managing track datasets (the GTrack ecosystem, https://gtrack.no), a methodology for building dynamic web-tools rapidly aimed primarily towards prototyping (Galaxy ProTo, https://github.com/elixir-oslo/proto), using only python code.
  • A national database of DNA variation of Norwegian individuals
  • Various collaborative efforts, typically providing infrastructure solutions for locally developed research software. Examples include tools for annotating cancer-related DNA variants and software for analysing adaptive immune receptors and repertoires using Deep Learning.
  • Core DevOps activities including operation of services from Infrastructure as a Service (IaaS) level and up, both using physical hardware and cloud resources; GitHub-centered software development, build and deployment infrastructure; containerization technologies (Docker, Podman, ...), package management (Conda, PYPI, Poetry...), relevant Open Source contributions, High-performance computing (HPC) job execution, etc. Note that low-level system administration will be mostly handled by the University Center for Information Technology (https://www.usit.uio.no/english/ ).

We are looking for system developers, DevOps engineers and/or strong bioinformaticians. A solid computational experience/background is required. The applicant should be motivated in working in an academic setting with development and operation of infrastructure and software, supporting Life Science research activities. Interest and motivation with learning and making use of various cutting-edge technologies is important. A background in bioinformatics is a plus, but not a requirement. Exact allocation of work tasks and projects will be dynamically determined based on the match of the candidate competence and motivation with arising needs.

Qualification requirements

Relevant master degree or above in informatics or bioinformatics from college or university - relevant experience can weigh up for lack of formal education.

Due to the varied technologies used in various projects and solutions, there are no strict competence requirements.

Important competence areas include:

• Professional software development experience in Python or Java. JavaScript experience is a plus, but will not be used for core development.
• Experience in Test-Driven Development (TDD), Agile methodologies, Design Patterns, and System architecture
• Open Source development experience, including git/GitHub-based version control, participation in Open Source communities, code contribution, etc.
• DevOps experience, including continuous integration and deployment: Jenkins, Travis CI, or similar
• Linux experience, including software dependency management and service-level operations.
• Workflow development/design in High Throughput Sequencing/Systems Biology, etc., in e.g. CWL, Galaxy, or similar workflow engines
• Scientific programming/statistics (NumPy, R, etc.)
• Experience with container platforms (Docker, Podman, Kubernetes etc.), and package management (Conda/BioConda, Pypi, Poetry, etc.)
• Database management and architecture
• Web front-end development
• Excellent communication skills in English, both oral and written.

Personal skills

• Good problem-solving capabilities
• Being self-driven and having the ability to work independently, as well as being a team player

We offer

• Salary NOK 542 400 - 640 200 per annum depending on qualifications in a position as Senior Engineer (position code 1181), depending on qualifications
• Stimulating, challenging and friendly work environment
• An organization in continuous development with ambitious goals
• Membership in the Norwegian Public Service Pension Fund
• Attractive welfare benefits

How to apply

The application must include:

• Application letter
• CV (complete overview of education and work experience)
• Copies of educational certificates, transcript of records and letters for recommendation
• Names and contact details of 2-3 references (names, relation to candidate and telephone number)

The application with attachments must be delivered in our electronic recruiting system. Please note that all documents should be in English (or a Scandinavian language).

Formal regulations

Interviews with the best qualified candidates will be arranged.

According to the Norwegian Freedom of Information Act (Offentleglova) information about

the applicant may be included in the public applicant list, also in cases where the applicant has requested non-disclosure.

Contact information

For more information about the position contact the:

• Director of the Centre for Bioinformatics, Prof. Eivind Hovig at +47 93069881, ehovig@ifi.uio.no

For questions regarding our application system, please contact HR Senior Adviser Torunn Standal Guttormsen, phone:+47 22854272, email: t.s.guttormsen@mn.uio.no

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