System developer at the NGI-Uppsala SNP&SEQ Technology Platform

Uppsala University, Department of Medical Sciences

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 45,000 students, more than 7,000 employees and a turnover of around SEK 7 billion.

Are you interested in the rapidly growing field of biotechnology? Would you like to work alongside researchers and bioinformaticians in a dynamic and creative atmosphere at one of Europe’s largest facilities for DNA sequencing? As a system developer at the SNP&SEQ Technology Platform, you will participate in developing solutions to optimize the flow of large-scale genotyping and sequencing data from our instruments to researchers.

The SNP&SEQ Technology Platform (SNP&SEQ) at Uppsala University is part of the Genomics Platform at SciLifeLab. With its modern state-of-the-art instrumentation for SNP-genotyping and next generation sequencing (NGS), SNP&SEQ offers service to users within Swedish academia and industry, as well as to international users. Our multidisciplinary team of project coordinators, research engineers, bioinformaticians, system developers, system administrators, and researchers work closely together to provide access to cutting-edge technologies for genomics research. Each year, >300 terabases of sequencing data are generated from >20,000 samples and >25 billion genotypes are generated from >50,000 samples. For more information about SNP&SEQ, its staff and services, please visit: https://snpseq.medsci.uu.se/

The SNP&SEQ is part of the Department of Medical Sciences, a large clinical department with approximately 250 persons employed and more than 300 persons affiliated with the University Hospital. More information about the department can be found here: www.medsci.uu.se

We are seeking a system developer to join our Systems group in maintaining, optimizing, and developing the various systems used in laboratory and bioinformatic processes. These include the automation of data handling and analysis; tracking of samples, steps and reagents in laboratory workflows; documentation management; and visualization of key performance indicators (KPI). SNP&SEQ works according to the European quality standard ISO/IEC 17025 and is accredited by SWEDAC as a testing laboratory for genotyping and sequencing. All of the work carried out at SNP&SEQ is performed with focus on providing service of the highest possible quality.

Job description: Your main responsibilities will be development, deployment and maintenance of the IT systems used within the facility for managing large-scale genotyping and sequencing data. Importance is placed on automation and information security. Your work tasks will include the following:

• Design and develop open-source systems for processing and analyzing data in the petabyte range.
• Create smart integrations with our LIMS (Laboratory Information Management System).
• Support internal systems at the SNP&SEQ technology platform.
• Develop existing DevOps solutions based on e.g. Ansible and GitLab.
• Establish, maintain and validate documentation of systems.
• Plan and purchase hardware and software.
• Cooperate with staff at the Uppsala University IT Department, UPPMAX and other SciLifeLab units.

Development within the platform is mainly carried out using Python. Since the operations at the SNP&SEQ Technology Platform are accredited by SWEDAC, there is an emphasis on documentation and version control.

Qualification requirements:

• University degree in computer science, IT or equivalent discipline.
• A minimum of 5 years documented work experience in systems development.
• Excellent programming skills in Python or similar high-level language.
• Ability to quickly learn new skills.
• Experience with Git.
• Thorough understanding of information security.
• High proficiency in a Unix/Linux environment.
• Excellent verbal and written communication skills in English.

We are looking for a person with a high degree of self-motivation, attention to detail, sense of responsibility, and ability to work both independently and in a team. Emphasis will be put on personal qualities such as a positive attitude and ability to work in a team.

Meriting skills: In addition to the qualification requirements listed above, we are happy to see previous experience from or knowledge in one or more of the following areas:

• Agile methods/scrum.
• Documentation and project management tools such as Confluence and JIRA.
• Software deployment methods (e.g. Ansible) and continuous integration.
• Computer clusters and distributed systems.
• Virtual environments, e.g. Docker.
• The ELK stack or similar log processing system.
• Familiarity with methods and applications in molecular biology and genetics.
• Good verbal and written Swedish communication skills.

Salary: Individual salary.

Starting date: As soon as possible or as otherwise agreed.

Type of employment: Permanent position with a six-month probation period.

Scope of employment: 100%

For further information about the position please contact: Head of unit, Ulrika Liljedahl, Ulrika.Liljedahl@medsci.uu.se.

Please submit your application by 19 October 2021, UFV-PA 2021/3490.