Computational Oncology Group

Senior Bioinformatics Engineer – Informatics Infrastructure

Senior Bioinformatics Engineer – Informatics Infrastructure

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 have expertise in software architecture and infrastructure development — a passion for mission-driven work? Do you want to be an important contributor to a team that includes computational biologists, software engineers, and data curators? If so, could be our next Bioinformatics Engineer.

As a member of our Informatics & Biocomputing team, you’ll work closely with scientists and engineers to support research projects in cancer and other genetic diseases. The work includes prototyping and evaluating solutions to support the harmonization and sharing of biomedical data (e.g., genomic, clinical, and imaging data). You’ll build systems to facilitate storage, management, and analysis of data via cloud, workflow, and containerization technologies. Ideal candidates will be enthusiastic about developing applications, processes, and standards that enable open, collaborative, and reproducible biomedical research.

What you’ll do: 

  • Design reusable architecture for cloud-based data storage and sharing among research networks.
  • Build scalable infrastructure to support data transformation and processing pipelines as reproducible workflows in multiple cloud environments.
  • Design, document, and implement new web APIs for internal and external services.
  • Work with Sage scientists and engineers to develop common strategies for the end-to-end management of large clinical and genomic data sets.
  • Work with the Sage platform engineering team to improve and extend existing products, including integration with third party services.
  • Engage with global research, industry, and standards development communities to keep abreast of new technologies and best practices.

We’d love to hear from you if: 

  • You have a PhD in Computer Science, Bioinformatics, Computer Engineering or related computational field and 1+ years of relevant job experience, or an MS and 4+ years of relevant job experience, or a BS and 7+ years of relevant job experience.
  • You’re enthusiastic about open science, collaboration, and reproducible research.
  • You can communicate effectively and efficiently with diverse audiences.
  • You’re proficient with collaborative development and version control systems (e.g. git).
  • You’re proficient in container technologies such as Docker.
  • You have experience using configuration management (e.g. Chef, Puppet, Ansible) or orchestration (e.g. CloudFormation, Terraform) tools.
  • You have experience with container orchestration systems (e.g., Kubernetes, Mesos).
  • You have experience implementing and deploying RESTful or GraphQL API web services.

Preferred, but not required:

  • You have experience with one or more workflow execution framework (e.g., Airflow, Argo, Luigi) or workflow standards relevant to the genomics community (e.g., CWL, WDL, Nextflow).
  • You’re familiar with graph databases, graph query languages (e.g., Cypher, SPARQL) and search engine technologies (e.g., Elasticsearch, Solr).
  • You’re familiar with at least one industry-standard programming language for developing front end applications (e.g., Java, PHP, Python, JavaScript/TypeScript).
  • You have experience working with biomedical (including genomic or clinical) data.

In light of recent concerns of Covid-19, all interviews will be conducted remotely, and most positions will be remote through at least June 30, 2021. The option to work on-site at our Seattle office prior to June 30, will be considered upon request.

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-intensive research for the advancement of human health. Data-intensive 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.

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