Bioinformatician with focus on systems development, NGI Uppsala, SNP&SEQ - Hiring in process/Finished, not possible to apply

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 across the unit.

Duties
Your responsibilities will include, but not me limited to:

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

Examples of 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.

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

Requirements

• University degree in bioinformatics, computer science, IT, or a related field.
• At least three years of documented professional experience in bioinformatics-related system development.
• Excellent knowledge of Python or similar programming languages.
• Experience using Git for version control.
• Ability to quickly learn new skills.
• High proficiency in Unix/Linux environments.
• Excellent verbal and written English skills.

Additional qualifications

In addition to the qualification requirements listed above, we also value previous experience in one or more of the following areas:

• Doctoral degree including bioinformatics with a focus on genomics, genetics, or similar area
• Experience in developing data processing pipelines, such as Nextflow or similar systems.
• Computer clusters and distributed systems.
• Virtual environments, e.g., Docker or Apptainer.
• Methods for software deployment (e.g. Ansible) and continuous integration.
• Familiarity with methods and applications in molecular biology and genetics.
• Understanding of information security.
• Agile methodologies/Scrum.
• ELK stack or similar log management systems.
• Experience in LIMS development.
• Experience in data management with public databases for FAIR data handling, such as ENA or ArrayExpress.
• Experience working in quality-assured environments, e.g. according to ISO 17025 or ISO 27001.
• Good verbal and written Swedish skills.

About the employment
The employment is a permanent position (6 months probationary period may be applied). Scope of employment 100 %. Starting date 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

Please submit your application by 29th of September 2025, UFV-PA 2025/2703.

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