Data & Tooling

Research Software Engineer

Research Software Engineer

At Sage Bionetworks, we believe that we can learn more by learning from each other. We develop and apply open practices to data-driven research for the advancement of human health. We are working to establish actionable biomedical observations through the reliable analysis and responsible sharing of representative data. By improving the way scientists collaborate and by increasing the reliability of research, we will improve human health.

Do you want to be an enthusiastic contributor to a team of problem solvers – computational biologists, software engineers, and data scientists? Do you have software development experience and a passion for mission-driven work? If so, you could be our next Research Software Engineer.

[DPE] Data & Tooling Department – Data Processing & Engineering Team

The Data & Tooling Department at Sage provides technical solutions that make it easier for biomedical researchers and data scientists to get their job done.  As part of the Data Processing & Engineering team, our mission is to empower Sage Bionetworks and our communities to do effective and modern data processing / analysis.  We strive to make data more accessible by designing and building data pipelines that are responsible for the processing and harmonization of hundreds of terabytes of raw data into usable information for our downstream users. We partner with research teams to build these pipelines for projects in cancer, neurodegenerative disease research, clinical informatics, and other bioinformatics and healthcare domains.

Your Role

You will build out and maintain components in our biomedical and open data ecosystem, contribute to team-science use cases, and develop implementations utilized by researchers across multiple biomedical areas: from oncology to COVID-19.  Types of projects/packages you have a chance to contribute to:

  • Systems that facilitate the storage, management, and processing of data via cloud, workflow, and containerization technologies in support of large data collaborative initiatives and data management projects.
  • Actively developed open-source codebases and pipelines for data validation and dissemination.
  • Workflow orchestration – centralization of data processing at Sage Bionetworks.
  • Development or execution of pipelines as reproducible workflows on terabytes of data using cloud infrastructure.

By interacting with multiple communities across the National Institutes of Health (NIH) or the Global Alliance for Genomics & Health (GA4GH), you will also have endless opportunities to learn from, contribute to, and accelerate biomedical discovery.

Here’s what you’ll do:

  • Contribute to the development of tools and applications that facilitate tracking, scalability, reproducibility, or processing of data and computational analyses in large scale scientific collaborations.
  • Work with scientists, software developers, project managers, and the Sage platform engineering team to improve products like Synapse (synapse.org), in-house applications, or third-party integrations that are part of our data platform ecosystem
  • Contribute to technical documentation to support users and developers.
  • Sometimes participate in and monitor the development of external groups and communities to stay informed on best practices and standards.
  • Participate in code reviews and provide feedback on code across the organization.
  • Use packages (e.g pandas) to build tools that interact with biomedical data combined with Python frameworks (e.g pytest) to ensure tool reliability.

We’d love to hear from you if you:

  • Have passion for open science, collaboration, and reproducible research and/or enthusiasm about applying modern technologies to accelerate scientific progress
  • Have an MS in Computer Science, Bioinformatics, Software Engineering or related field and 2+ years of relevant job experience, or a BS and 4+ years of relevant job experience.
  • Have an intermediate proficiency with collaborative development and version control systems (e.g. git).
  • Have an intermediate proficiency with software development life cycles and scripting/package development in Python and optionally R.
  • Possess effective verbal, written, and organizational skills with the ability to communicate with a variety of technical and non-technical collaborators.
  • Have an intermediate proficiency with continuous integration (CI), continuous development (CD), and testing frameworks.

Also Preferred BUT NOT Required

  • Comfortable working in a cloud based IT environment or HPC/cluster environments.
  • Experience working with biomedical (including genomic, imaging, or clinical) data.
  • [DPE] Experience working with container technologies such as Docker or Singularity.
  • [DPE] Experience working with data pipeline and/or workflow automation tools/languages used in industry (e.g. Airflow, Prefect, Luigi) or in research (e.g. Nextflow, CWL, Snakemake)

 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.

Sage embraces diversity, equity and inclusion. We are committed to pay parity and making our salary ranges available to all employees. We invite you to apply and we welcome a conversation. We are based in Seattle, WA, and collaborate broadly throughout the world.

Sage provides a flexible work environment and will accommodate requests for geographically remote work with manager approval. Sage will also accommodate local employees who choose to work remotely from the Washington area with the option to come into the office on a flexible schedule.

All interviews will be conducted remotely at this time.

This is a Professional level position on our Technical and Engineering Professional career ladder, with a compensation range of $89,735 – $143,575. Actual compensation is dependent upon experience.