Job vacany: Senior Engineer/Bioinformatician at Oslo University Hospital
"Are you a bioinformatician looking for a multifaceted position? Do you enjoy connecting with people, looking for variation in daily tasks, and having a service minded-attitude? Come and join the Bioinformatics Core Facility as our senior bioinformatician/coordinator. We have an open 3-years position with the possibility of extension in a competent and interdisciplinary research environment."
The Bioinformatics Core Facility is funded by the South-East Health region (HSØ), and is an approved core facility for all HSØ institutions, as well as for the University of Oslo. We are located at the Institute for Cancer Research at Radiumhospitalet, formally organized under the Department of Core Facilities at Oslo University Hospital.
Here we reside in a basic, translational, and clinical research environment, together with 6 other core facilities offering cutting-edge technologies, services and analysis support (https://www.ous-research.no/corefacilities/). The Bioinformatics Core Facility is tightly connected to the Oslo node of the national Norwegian ELIXIR bioinformatics infrastructure (which is also a part of the European bioinformatics infrastructure (ESFRI). The core facility also collaborates with the Bioinformatics Center at the Department of Informatics, the University Center for Information Technology (USIT), as well as the Oslo Centre for Biostatistics and Epidemiology (OCBE) - all located at the University of Oslo.
Our work focuses on providing high-quality services on a wide range of data analysis topics. We work primarily with -omics data (genomics, transcriptomics, epigenomics, and proteomics), and our services also include workflow development/scripting, support using national web- and other services, biostatistics, access to databases and specialized license-based software to mention some. The majority of projects are related to human health research, as the core facility is immersed in Norway’s strongest cancer research environment.
The candidate will spend approximately 80 % of their time working on research-related service projects on behalf of users. This includes providing bioinformatics analysis of their data, developing custom workflows, and researching state-of-the-art analysis strategies to ensure optimal analysis. Approximately 20% of their time will be used for coordinating our daily activities together with the core facility management and personnel. This includes answering incoming requests and providing price quotes, invoicing, and supporting the management with reports and applications to our funding agencies. Some outreach activity to relevant research institutions is to be expected. Finally, there will be joint Bioinformatics Core Facility / ELIXIR helpdesk activities. This encompasses monthly joint meetings at the University of Oslo and assisting with the national ELIXIR helpdesk support system.
Oslo University Hospital is a workplace with great diversity. We believe this is absolutely crucial to solving the tasks required of us. We therefore want this diversity to be reflected among the applicants for our positions and encourage everyone to apply regardless of who you are and what background you have.
Duties and responsibilities:
The successful candidate will participate in providing bioinformatics data analysis as requested by the users. We handle all omics data, but most projects use bulk and single-cell RNA, exome and whole genome sequencing, and epigenetic data. We also see an increased demand for spatial data (RNA/protein) analysis and high-dimensionality mass/flow cytometry data. Services may vary from quality control of raw data to in-depth exploration of biological patterns. Common analyses include variant calling on tumor-normal pairs, differential gene expression of bulk and single-cell data, and clinical annotation of analysis outputs. We also offered development of custom solutions, long-term support for large projects, and support for users setting up their analysis environments within Tjenester for Sensitive Data (TSD), and advice for Data Management Plans.
The successful candidate will support the core facility management with everyday tasks related to our users. This encompasses answering any incoming requests, researching and setting up suggestions for analysis workflows, and generating price quotes and contracts. We also do yearly outreach efforts where we visit relevant research environments and present our services. Finally, the candidate will support the management by providing the data foundation for reports and applications.
There will be shared activity between The Bioinformatics Core Facility and the Oslo node of ELIXIR with respect to the ELIXIR helpdesk. Here, the candidate will attend monthly meetings, the yearly ELIXIR all-hands meeting, and answer any incoming tickets to the helpdesk system when relevant. In this setting, the candidate will get to interact with key personnel and competence from both USIT/TSD and ELIXIR Oslo being part of a resourceful network.
- A master’s degree with 5 years of experience in the field of bioinformatics or similar. A PhD degree in a relevant field is beneficial.
- Knowledge of UNIX, Python and R, and preferably one more workflow language (e.g. NextFlow)
- Experience with high-performance computing (HPC) and containers (Docker, singularity, biocontainers or similar)
- Advanced bioinformatics skills and experience with handling large biological datasets
- Excellent verbal and written communication skills (English)
- Excellent documentation skills to support FAIR principle.
- Good grasp of basic molecular biology
- Experience with machine learning
- Experience with workflows provided today by the core facility (described above)
- Some experience with UNIX/Linux systems with respect to software installation and similar
- Experience with database installation and maintenance
- The candidate should be able to work independently as well as a part of the team
Good communication skills are required as the successful candidate is expected to interact closely with the members of core facility and research groups
- A 3 years position with the possibility of extension in an interdisciplinary and international research environment
- Variation in the daily work tasks
- Possibility to grow and develop competencies in different areas
- A team of supportive colleagues