About the position

A 50 % position as Head Engineer, is available for a systems developer/sysadmin. The position will be part of the team of the national ELIXIR project, at the Oslo node, having office at Department of Informatics, University of Oslo. Starting date as soon as possible.

The position is permanent contingent to external funding.

The position will be located at the University of Oslo. There will also be possibilities for remote working parts of the time. Languages: Norwegian or English.

The work will be conducted in the context of the ELIXIR Norway project, which is the Norwegian node of the established European bioinformatics research infrastructure project. We provide services to users in the Oslo region, with an emphasis on the biomedical community. These services are coordinated with the Helse Sør-Øst Core facility of bioinformatics.

Job Description

The successful candidate will be expected to be part of the operations and service team, as well as to undertake development tasks within the Elixir.no/Bioinformatics core facility infrastructure. An important such task will be to operate and further develop bioinformatics services hosted by the Oslo node of ELIXIR Norway, including sysadm tasks on the servers, operation of various databases, web-based solutions, and other infrastructure. These services include:

• The Genomic HyperBrowser, a Galaxy-based software system catering to statistical analyses of massive genomic datasets, which is also a Norwegian contribution towards ELIXIR Europe. The Galaxy framework, is a leading web-based framework for accessible, reproducible and transparent biomedical research.
• The Oslo node of the National e-Infrastructure for Life Science, NeLS, which serves bioinformatics tools and pipelines within the abovementioned Galaxy framework.
• The Galaxy Prototyping Tool API (Galaxy ProTo) an extension of Galaxy that provides an unofficial alternative tool building methodology, heavily used by the Genomic HyperBrowser.
• Various databases with web frontends, including MirGeneDB that hosts curated miRNA.
• MirMiner, which is a novel pipeline for miRNA prediction, implemented with “make”.
• A custom-built development infrastructure, making use of GitHub for version control, Syncthing for remote development, and GoCD for continuous deployment of Galaxy/HyperBrowser instances.
• Development and operations of the new Elixir Norway web pages, based upon CMS Made Simple.

Qualification requirements

We are seeking a candidate with a Bachelor degree in computer science or similar - relevant experience can weigh up for lack of formal education. The candidate should have solid experience in sysadmin work, web operations and development, database admin and development, development infrastructure operations, as well as good programming skills.

Required skills:

Sysadmin:

• Thorough experience administrating Linux servers, as well as traditional and cloud-based VMs, and Docker
• Experience and preferably training in Galaxy administration
• Development using BASH, Make, GCC, Autotools, etc.
• Command line know-how and trouble-shooting experience
• Experience with security setup (SSH, SSL certificates, etc.)
• Web servers (Apache)
• File system setup, specifically experience with the CernVM File System
• Package distribution (Yum, PYPI, Conda, BioConda)

Web development:

• General Web development (CSS, Javascript, Less, Flask, PHP)
• CMS systems (CMS Made Simple)
• Template languages for web development (Jinja, Mako, Smarty, …)

Database admin and development:

• Knowledge of SQLite, Mysql, and Postgresql
• Experience in developing and operating database solutions

Development infrastructure operations:

• Version control (Git / GitHub)
• Other relevant systems include Syncthing and GoCD

Programming:

• Detailed knowledge of the Galaxy framework code base is a big plus (preferably also with a thorough understanding of Galaxy ProTo and the Galaxy interfaces of the Genomic HyperBrowser, as the successful candidate will be the main developer of these).
• Experience in development of bioinformatics pipelines is a plus, as the successful candidate will be responsible for operations and further development of, among others, the MirMiner pipeline.
• A firm grip of Python is a necessity
• Other relevant development languages include Bash, Javascript, and PHP.

General:

• Excellent communication skills in English, both oral and written.
• Being self-driven and having the ability to work independently, as well as being a team player

We offer

• salary NOK 576 100 – 631 700 per annum depending on qualifications in a position as Head Engineer, position code 1087
• attractive welfare benefits and a generous pension agreement, in addition to Oslo’s family-friendly environment with its rich opportunities for culture and outdoor activities

How to apply

The application must include:

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

The application with attachments must be delivered in our recruiting system.

Interviews with the best qualified candidates will be arranged.

Foreign applicants are advised to attach an explanation of their University’s grading system. Please remember that all documents should be in English or a Scandinavian language.

Formal regulations

According to the Norwegian Freedom and 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.

In accordance with the University of Oslo’s equal opportunities policy, we invite applications from all interested individuals regardless of gender or ethnicity.

The University of Oslo has an agreement for all employees, aiming to secure rights to research results.

Contact information

• Professor Eivind Hovig, +47 93069881, e-mail ehovig@ifi.uio.no

For technical questions regarding the recruitment system, please contact:

• HR Adviser Torunn Standal Guttormsen, +47 22854272, e-mail t.s.guttormsen@mn.uio.no

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