Data Engineer for high throughput sequencing core facility

vor 2 Wochen

Bern, Schweiz University of Bern Vollzeit
• University of Bern, Next Generation Sequencing Platform (NGSP)
• Start of employment: per immediate or by agreement
• 12 months with option for extension/conversion to permanent contract
The NGSP is one of five official core facilities at the University of Bern. The mandate of the facility is to support researchers in all aspects of their high-throughput sequencing projects from nucleic acid extractions to data generation from short-read and long-read sequencers, post-run processing tasks, data storage, and transfer. As we expand our data team and improve our IT infrastructure, we seek a skilled data engineer with software development experience and creativity to join our team.

Tasks
  • Data Management: Ensure efficient handling, storage, and retrieval of large sequencing datasets, implementing best practices for data integrity and security.
  • Laboratory Information & Project Management Systems: Contribute to design, implementation, maintenance, and improvement of our Laboratory Information/Project Management Systems to support lab operations.
  • Pipeline Development & Automation: Design, develop, and maintain scalable data processing pipelines for tasks such as automated data delivery, quality control, and analyses.
  • Software Development & Open-Source Contribution: Actively develop and maintain software solutions, with encouragement to contribute to open-source projects where applicable.
  • Collaboration & Support: Work closely with scientists, bioinformaticians, and facility scientists to understand project data processing needs and provide technical support.

Requirements
  • Education: University degree in Computer Science, Bioinformatics, or equivalent education or training.
  • Proficiency with programming/scripting languages such as Python, Java, and Ruby on Rails.
  • Knowledge of HPC environments, job scheduling systems (SLURM), and cloud-based storage solutions.
  • Strong problem-solving skills and ability to troubleshoot complex technical issues.
  • Excellent communication skills and the ability to work independently as well as collaboratively in a multidisciplinary diverse team.
  • Fluency in English. Any other language is an asset.
  • Experience with workflow managers (Snakemake/Nextflow) would be an asset.
  • Familiarity with relational and non-relational databases would be beneficial.
  • A desire to learn about Linux system administration.

We offer
  • Cutting-edge and collaborative research environment: Work in a highly motivated team of scientists, IT professionals, and bioinformaticians in a facility using state-of-the-art sequencing technologies and on projects from a multitude of different life science fields of research.
  • Career growth: Opportunities for professional development and training in bioinformatics, data engineering, and genomics.
  • A varied and interesting range of tasks with flexible working hours and mobile working with home office option.
  • Progressive employment conditions and social benefits in accordance with cantonal guidelines.

Application and contact
For more information or questions please contact the head of the NGSP at pamela.nicholson@unibe.ch or 031 684 22 85.

Please send your application as one pdf document to: nadine.bucher@unibe.ch by the 7th of April 2025.

We look forward to hearing from you


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