Systems developer at NGI-Uppsala, SNP&SEQ Technology Platform

Published: 2022-12-16

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 54,000 students, more than 7,500 employees and a turnover of around SEK 8 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 be involved in maintaining the infrastructure that enables the flow of large-scale genotyping and sequencing data from our instruments to researchers.

The SNP&SEQ technology platform is part of the National Infrastructure for Genomics (NGI) at SciLifeLab in Uppsala. SNP&SEQ offers services with modern large-scale methods and applications in sequencing (NGS), SNP genotyping and proteomics to users within Swedish academia and industry, and also to international users. The business consists of a multidisciplinary group of researchers, project coordinators, research engineers, bioinformaticians, system developers and system administrators. Annually, the platform generates > 300 terabases of sequence data from > 20,000 samples, > 25 billion genotypes from >30,000 samples and contributes to >100 publications. As a member of the National Genomics Infrastructure (NGI), we benefit from a dedicated cluster with more than 3000 cores. More about SNP & SEQ's operations and NGI can be read at: https://snpseq.medsci.uu.se/ and https://ngisweden.scilifelab.se/

SNP&SEQ is formally a part of the Department of Medical Sciences which is a large clinical department with about 250 staff and over 300 people who are connected via Uppsala University Hospital. You can read more about the work of the department at www.medsci.uu.se.

Read more about our benefits and what it is like to work at Uppsala University.

Duties
We are seeking a systems developer to join our Systems group in expanding our data processing pipelines and Laboratory Information Management System (LIMS). Because of the sensitive nature of the data we handle there is a strong focus on information security, automation and traceability. As such we work according to the European quality standard ISO/IEC 17025 and are accredited by SWEDAC as a testing laboratory for genotyping and sequencing. We continuously strive to improve our development procedures and keep up with the state of the art in terms of CI/CD, version control and documentation.

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

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.

Additional qualifications
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:

• Java, C or C#
• Databases (e.g. MySQL)
• 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, genetics or bioinformatics
• Good verbal and written Swedish communication skills

About the employment
The employment is a permanent position, 6-month probationary period will be applied. Scope of employment 100 %. Starting date as soon as possible or as agreed on. Placement: Uppsala

For further information about the position please contact: Head of systems group: Kristina Larsson, +46 70-1679451, kristina.larsson@medsci.uu.se or group coordinator Matilda Åslin, matilda.aslin@medsci.uu.se

Please submit your application by February 1, 2023, UFV-PA 2023/4963.

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Submit your application through Uppsala University's recruitment system.

Placement: Department of Medical Sciences

Type of employment: Full time , Permanent position

Pay: Individuell lönesättning

Number of positions: 1

Working hours: 100 %

Town: Uppsala

County: Uppsala län

Country: Sweden

Union representative: Seko Universitetsklubben seko@uadm.uu.se
ST/TCO tco@fackorg.uu.se
Saco-rådet saco@uadm.uu.se

Number of reference: UFV-PA 2022/4963

Last application date: 2023-02-01