Bioinformatician with focus on systems development, NGI Uppsala, SNP&SEQ

Are you interested in working close to cutting-edge research and supporting a broad scientific community? Do you thrive in a dynamic and forward-looking environment where you can both use and develop your technical skills? Then this position may be right for you.

The Department of Medical Sciences (IMV) is a large clinical department with approximately 250 employees and over 900 people affiliated through the Academic Hospital. The department has a broad research profile with strong research groups in various areas. The research takes place in close connection with the clinical activities at the Academic Hospital and includes both basic studies on disease causes and the development and evaluation of improved diagnostics and new treatment methods. More about the department's activities can be found at www.medsci.uu.se.

The SNP&SEQ Technology Platform at IMV is part of the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala. We provide large-scale sequencing (NGS), SNP genotyping, and proteomics services to Swedish academia, industry, and international users. Our multidisciplinary team includes researchers, project coordinators, research engineers, bioinformaticians, system developers, and system administrators. Each year, we process more than 60,000 samples and generate over 400 Terabases of data. More about our activities and services can be found at: https://www.uu.se/forskning/snpseq and https://ngisweden.scilifelab.se/

We are proud to deliver high-quality data and are accredited by SWEDAC as a testing laboratory under the ISO/IEC 17025 quality standard.

We are now looking for a technology-driven bioinformatician to join our Data Operations group. The group at the interface of bioinformatics and IT, ensuring smooth and efficient data handling within the unit.

Duties

Your responsibilities will include:

• Designing, developing, and maintaining open-source systems for processing and analyzing large-scale genomics data.
• Managing data on our dedicated high-security compute cluster Miarka at UPPMAX, as well as on local servers.
• Automation of data handling and integrating systems for laboratory tracking (samples, steps, reagents), document management, and KPI visualization.
• Developing and supporting internal systems, including LIMS (Laboratory Information Management System) and existing DevOps solutions (e.g., Ansible, GitLab).
• Establishing, maintaining, and validating system documentation.
• Collaborate closely with Uppsala University IT, UPPMAX, and other SciLifeLab units (e.g. NBIS).

Other tasks may be added depending on needs and competence.

The systems and tools you will work with include Arteria (https://github.com/arteria-project), CheckQC (https://github.com/Molmed/checkQC), nf-core pipelines (https://nf-co.re/), and Nextflow.

Requirements

• University degree in bioinformatics, computer science, IT, or a related field.
• At least three years of documented work experience in bioinformatics-related systems development.
• Excellent knowledge of Python or a similar programming language.
• Experience in developing pipelines for data processing and management, such as Nextflow or similar systems.
• Knowledge of methods and applications in molecular biology and genetics.
• Experience using Git for version control.
• Ability to quickly learn new skills.
• Experience working in a Unix/Linux environment.
• Excellent verbal and written English skills.

We are seeking a candidate who is detail-oriented, quick to learn new skills, and able to work both independently and collaboratively.
In addition to the qualification requirements listed above, we highly value prior experience in one or more of the following areas

Särskilt meriterande krav

• Experience in using computer clusters and distributed systems.
• Experience in virtualized environments, e.g., Docker or Apptainer.
• Experience with software deployment and infrastructure automation, e.g. Ansible, and CI pipelines.
• Experience with modern software engineering practices, such as code reviews, testing, automated testing, and CI/CD workflows.

Additional qualifications

• Doctoral degree including bioinformatics with a focus on genomics, genetics, or a related area
• Establishing and maintaining system documentation and test specifications.
• Understanding of information security principles.
• Working with Agile methodologies/Scrum.
• Experience in LIMS development.
• Experience in data management and FAIR data handling, including public repositories such as ENA or ArrayExpress.
• Experience working in quality-assured environments, e.g. in accordance with ISO 17025 or ISO 27001.
• Good verbal and written Swedish skills.

Highly preferred qualifications

The employment is a permanent position (a six-month probationary period may be applied). Scope of employment 100 %. Starting date June 1, 2026 or as agreed. Placement: Uppsala

For further information about the position, please contact: Kristina Larsson, head of Data Operations, kristina.larsson@medsci.uu.se, Ulrika Liljedahl, head of unit SNP&SEQ, ulrika.liljedahl@medsci.uu.se.

Application procedure

In this recruitment, we have replaced the personal letter with questions that you answer in connection with your application. The answers will be used as part of the selection process. In addition, the following documentation is required:

• CV
• Documents that prove the requested competence