Software Development Engineer II

Overview

Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington.

With a track record of global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy and COVID-19 vaccines, Fred Hutch has earned a reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality.

At Fred Hutch we value collaboration, compassion, determination, excellence, innovation, integrity and respect. Our mission is directly tied to the humanity, dignity and inherent value of each employee, patient, community member and supporter. Our commitment to learning across our differences and similarities make us stronger. We seek employees who bring different and innovative ways of seeing the world and solving problems.

The McCrone Lab is seeking a Software Developer II for support of their cutting edge Nexstrain project. The Software Developer Engineer II (SDE II) will work on Nextstrain, an award-winning project for tracking infectious disease epidemics such as the SARS-CoV-2 pandemic, Ebola outbreaks, Zika spread in the Americas, seasonal flu, and other emerging and endemic pathogens. This position will augment our existing team to design, develop, maintain, operate, and support our software and services that empower research scientists and public health practitioners in the lab and around the world. Nextstrain was developed in collaboration with the Neher Lab at the University of Basel and provides tools for evolutionary analysis of pathogens and genomic epidemiology. We write open-source software in a public development style to power all parts of Nextstrain—bioinformatics, visualizations, analysis pipelines, data management, and more—and our analyses use open data whenever possible. We work with public health entities and scientists across the world, both formally and informally, to expand pathogen surveillance capabilities and to improve the automation and robustness of these analyses. Our goal is to empower the wider genomic epidemiology and public health communities to tweak our analyses, create new ones, and communicate scientific insights using the same tools we do. Our team provides opportunities for cross-disciplinary learning, drawing insights from scientists, public health practitioners, and fellow software developers. We believe in continuous learning and cultivating an environment where all members of the group help each other.

This position will be responsible for general software engineering and development work across the entire Nextstrain stack. This includes command-line applications for bioinformatics and data/workflow management (e.g. Augur, Nextstrain CLI), visualization applications for phylogenetics (e.g. Auspice), full-stack web applications for sharing analyses (e.g. nextstrain.org), workflows for data curation and analysis (e.g. ncov-ingest), runtimes for Nextstrain analyses (e.g. docker-base, conda-base), and internal tooling/infrastructure to support all of that. The SDE II performs testing, troubleshooting and debugging of application throughout the development process. This position reports to the Assistant Professor who leads the lab responsible for maintaining and enhancing NextStrain.

This role will have the opportunity to work partially at our campus and remotely.

Responsibilities

• Design, develop, test, document, and maintain software under a coherent ecosystem.
• Follow software development best practices to design and develop software features to meet end user specifications.
• Troubleshoots user issues and debugs the software.
• Assist in the analysis of application requirements as requested.
• Release new versions of packaged programs for installation by users and deploy new versions of hosted services to users.
• Configure and manage cloud infrastructure resources (e.g. AWS, Heroku, Terraform).
• Create, extend, and troubleshoot automated workflows (e.g. GitHub Actions, Snakemake, Nextflow, WDL).
• Participate in constructive code review processes with other team members.
• Support internal and external users of software projects via various communication channels.
• Create and maintain technical documentation.
• May be responsible for providing on-call support.
• Other