Bioinformatician/System administrator (Specialist engineer)

High-throughput sequencing (HTS) is a technology that allows for fast and cost-effective characterization of DNA. The Department of Medical Genetics at Oslo University Hospital is Norway’s largest medical genetics department with over 240 employees and state-of-the-art sequencing equipment dedicated to providing diagnostics for patients suffering from severe hereditary diseases. We are expanding our HTS-based service and are looking for a new colleague to develop and manage the IT-infrastructure and automation systems on which we run our genomics analyses. 

The Unit for HTS-diagnostics is responsible for developing new diagnostic analysis pipelines as well as software and methodologies that provide decision support when interpreting genetic data. The HPC-analyses of the genomic data (1.5 TiB per run of a sequencer) are primarily performed in the local NorSeq infrastructure, which is developed and maintained by NorSeq bioinformaticians, but also in Tjeneste for Sensitive Data (TSD), at the University of Oslo. In addition, various cloud services are used for development and testing. The scale and complexity of our IT-operations is increasing, and we need to strengthen the team that currently manages the NorSeq hardware and software infrastructure. The work in this position will be a combination of furthering the development and management of the infrastructure, as well as further developing the automation and data management routines for the computational pipelines used in diagnostics. This position is permanent and full-time.

We are a diverse, multi-disciplinary team of bioinformaticians, developers, molecular biologists and mathematicians seeking candidates who can contribute their experience and talent to further develop bioinformatics at Oslo University Hospital. For more background information and details about the team, please see the description at https://www.ous-research.no/digigen, http://about.ousamg.io and https://www.sequencing.uio.no/. Please contact the bioinformatics group coordinator Tony Håndstad at tony.handstad@medisin.uio.no or unit manager Knut Erik Berge at kberge@ous-hf.no for any questions. The deadline for applications is April 3rd and the position is available from that date and onwards. Note that the full suitability of a candidate will be given consideration in the selection and interview process.

Oslo University Hospital is a workplace with great diversity. We believe this is essential to perform the tasks required of us. Therefore, we pursue diversity among our job applicants and encourage everyone to apply regardless of who you are and what background you have.

Duties and responsibilities

• System administration of local IT infrastructure (Linux and Windows based), including installing, configuring, monitoring and trouble-shooting hardware (virtualized servers, storage, network) and software
• Management of TSD and cloud environments
• Automation of analyses, status monitoring, data and metadata management
• Configure and program against automation frameworks, LIMS (laboratory information management systems) and possibly lab robotics and other equipment
• Contribute to DevOps in the bioinformatics group
• Document systems and workflows

Professional Qualifications

• Experience with system administration of Linux servers, and deep knowledge of Linux/CLI
• Experience with management of computer networks, and use of virtualization and container technology (e.g. VMware, Docker, Singularity)
• Good scripting programming skills (e.g. Bash, Python)
• Interest in automation; knowledge of relevant frameworks (e.g. StackStorm or similar) is an advantage
• Interest in workflow and pipeline orchestration (e.g. Nextflow)
• Some experience with cloud administration and grasp of computer security is an advantage
• Excellent English communication skills, knowledge of Norwegian is a plus

Personal qualities

• An orderly and well-structured proactive mindset
• Demonstrated problem- and error-solving skills. Deep understanding of systems and ability to troubleshoot them
• Ability to work individually as well as part of a team
• Interest in learning the domain and contributing in a diagnostic and research setting
• While higher education and certifications are a plus, we welcome applications from interested learners who have practical tinkering experience and high standards

We can offer

• Work in an exciting and extremely fast-developing field with a high impact on healthcare
• Varied tasks, and autonomy to exercise a wide range of skills
• Flexible hours with possibilities for part-time remote work
• Highly competent and friendly colleagues to learn from
• Salary dependent on qualifications