Bioinformatician in pipeline development

Are you interested in working with pipeline development in bioinformatics, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a position as Bioinformatician in pipeline development at Uppsala University.

National Bioinformatics Infrastructure Sweden (NBIS) (nbis.se) plays an important role in advancing life science research in Sweden by providing expert support and developing cutting-edge bioinformatics infrastructure. Operating as a truly national initiative, NBIS employs more than 120 bioinformaticians, system developers, and data stewards across multiple locations in Sweden. It serves as the bioinformatics platform at SciLifeLab, a national resource that facilitates research in molecular biosciences by offering access to state-of-the-art technologies and technical expertise. With strong ties to data-producing facilities and ongoing collaborations with leading research groups, NBIS is ideally positioned to support world-class bioinformatics analyses. Furthermore, NBIS is the Swedish node in ELIXIR, the European infrastructure for biological information.

NBIS is seeking an experienced bioinformatician to support both Swedish and international projects. As part of our dynamic team, you will work closely with researchers to process large-scale biological data and contribute to advancing our data analysis infrastructure. Strong problem-solving skills, attention to detail, and the ability to troubleshoot complex bioinformatics pipelines are essential for success in this role. Flexibility and a willingness to learn are also important, as NBIS continually adapts to meet the evolving needs of the Swedish research community.

This position is based at Uppsala University at the ICM (Cell and molecular biology) department, within the creative environment of the SciLifeLab Uppsala node, "The Hub," where over 50 NBIS bioinformaticians, developers, and data stewards collaborate alongside other SciLifeLab facilities and research groups. At NBIS, you will be part of a team, with ample opportunities to share ideas, learn from colleagues, and grow professionally through internal courses and exciting projects.

Duties

Your responsibilities will include supporting various research projects with the development of their bioinformatics pipelines. This will involve developing, implementing, and optimizing bioinformatics workflows using Nextflow to process high-throughput data, such as genomic sequence data, mass spectrometry data, or expression data. You will be tasked with maintaining and improving existing pipelines, ensuring they meet performance, scalability, and reproducibility standards. Additionally, you will be expected to write clear, efficient, and well-documented code to support reproducible data analysis. Finally, you will contribute to the publication of scientific results and share your workflows through public repositories such as GitHub. Other types of bioinformatic analyses can also be included in your work duties, depending on your competences and what kind of projects we receive, although you can expect your work to be focused on pipeline development. NBIS also has an extensive course catalog and you will have the opportunity to participate in teaching at advanced level (PhD level and up).

Requirements

• PhD in Bioinformatics, Computational Biology, Computer Science, or a related field or equivalent professional experience (>5 years) of bioinformatics
• Proficiency in developing pipelines using Nextflow (preferred) or Snakemake, with demonstrable experience through self-developed pipelines available on code repositories (such as GitHub/GitLab/Bitbucket…; please provide a link to your repository as proof of expertise). This includes the ability to write, optimize, and troubleshoot complex pipelines for high-throughput data analysis.
• Hands-on experience with common bioinformatics tools
• Experience working in Unix/Linux environments and high-performance computing (HPC) systems (e.g. SLURM etc.).
• Excellent communication skills in both written and spoken English are required as is ability to collaborate with scientists of very different backgrounds.
• Emphasis will be placed on personal suitability for the position, such as ability to drive projects and work in a collaborative, yet service-minded environment.
• A willingness to learn new methods and an ability to acquire new skills is a requirement for this position.

Additional qualifications

• Experience with tools and technologies that promote reproducibility, such as containers (e.g., Docker, Singularity)
• Good understanding of common bioinformatics data formats and processing workflows.
• Experience of developing pipelines to nf-core standards.
• Strong ability in R or scripting languages such as Python is considered positive.
• Previous experience of working in a support function is also considered beneficial.
• Experience with GitHub, distributed version control, and code review.