Systems engineer – Bioinformatics

Systems engineer – Bioinformatics

We are seeking a Systems engineer – Bioinformatics in the Computational Oncology Group. As a member of our team, you will work closely with the scientists and associates in the Computational Oncology group at Sage Bionetworks to support various research projects in cancer. The work includes prototyping software tools and setting up cloud infrastructure to support the harmonization and sharing of biomedical data (e.g., genomic, clinical, and imaging data) and DREAM Challenges ( You will also interact with other scientists and engineers in the global biomedical research community to discuss and apply cutting-edge technologies to support scientific data coordination. Ideal candidates will be enthusiastic about the developing applications, processes, and standards that enable open, collaborative, and reproducible biomedical research.

Specific Responsibilities Include

  • Design and develop systems architecture for managing and computing clinical and biomedical research data types, using an in-house data-sharing platform and state-of-the-art cloud technologies.
  • Design computational infrastructure to support DREAM Challenges, including for job queuing, provisioning scalable compute, and tracking status.
  • Design and build bioinformatics pipelines, including for data processing and extract-transform-load (ETL) procedures; author workflows in standardized languages.
  • Collaborate with in-house software engineering team on development of new platform functionality; and prototype new tools, write documentation, and train users.

Basic Qualifications

  • BA/BS in Computer Science, Bioinformatics, Computer Engineering or related field with 3+ years of relevant job experience.
  • Proficiency in Python and working knowledge of R.
  • Proficient with collaborative development and version control systems (e.g. git).
  • Proficient in Unix OS and cloud (AWS, Google) environments.
  • Proficient in container technologies such as Docker.
  • Experience maintaining RDBMS and knowledge of SQL.
  • Experience with software development life cycles.
  • Experience developing data models.
  • Experience working with web services through RESTful APIs.

Preferred Qualifications

  • Experience developing tools and workflows using either Common Workflow Language (CWL) or Workflow Definition Language (WDL).
  • Experience with NoSQL and search engine technologies such as GraphQL, MongoDB, or Elasticsearch.
  • Experience building and deploying applications to production environments (including unit/integration testing, continuous integration, and packaging).
  • Experience working with biomedical data.

About Sage Bionetworks

Sage was founded in 2009 as a non-profit spinoff from Rosetta Inpharmatics (Merck) to pioneer open approaches to advancing biomedical research.  We further our understanding of human diseases by integrating diverse clinical, genomic, imaging, and real-time sensor data to better predict disease progression and response to interventions. We are based in Seattle, Washington, and collaborate broadly throughout the world. Sage offers a comprehensive benefits package.

Apply here.