Computational Oncology Group

System Engineer – Bioinformatics

System 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 (dreamchallenges.org). 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 Bionetworks is a nonprofit biomedical research and technology development organization that was founded in Seattle in 2009. Our focus is to develop and apply open practices to data-driven research for the advancement of human health. Data-driven research has become an important component of biomedicine, but it’s not always easy to understand how to apply computational approaches appropriately or how to interpret their results. Sage believes open practices can help. Our interdisciplinary team of scientists and engineers work together to provide researchers access to technology tools and scientific approaches to share data, benchmark methods, and explore collective insights, all backed by Sage’s gold-standard governance protocols and commitment to user-centered design. Sage is supported through a portfolio of competitive research grants, commercial partnerships, and philanthropic contributions.

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