Data & Tooling

Bioinformatics Engineer – Python Specialist

Bioinformatics Engineer – Python Specialist

Sage Bionetworks Culture

At Sage Bionetworks, our inclusive worldwide culture celebrates multiple approaches and points of view, driving innovation in knowing we gain knowledge by learning from each other.  By improving the way scientists collaborate with healthcare innovators and patients, we help to make science more effective and advance biomedicine.

The Informatics & Biocomputing (IBC) Team

The IBC team provides technical solutions that make it easier for scientists to get their job done. By partnering with scientists, product managers, and other bioinformatics and software engineers in the larger Data & Tooling group, we tackle projects in cancer and neurodegenerative disease research, clinical informatics, and other healthcare domains. We collaborate with research team members to identify use cases, define data models, implement tools, develop workflows, and manage cloud resources while adopting and promoting standards for open science.

Your Role

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, as well as a passion for findable, accessible, interoperable, and reusable (FAIR) data solutions in biomedical research? If so, you could be our next Bioinformatics Engineer.

You will engineer backend components to enable team science across the lifecycle of resource development and dissemination.  Interacting with multiple communities across the National Institutes of Health (NIH) and the Global Alliance for Genomics & Health (GA4GH) provide endless opportunities to learn from, contribute, and accelerate biomedical discovery.

You will design and build out components in our biomedical and open data ecosystem, think through team-science use cases, derive solution requirements, and develop implementations utilized by researchers across multiple biomedical areas: from oncology to COVID-19.  You will contribute to actively developed open-source codebases; interactive immuno-oncology results exploration (e.g., iAtlas portal); and pipelines for data validation and dissemination (e.g., powering the AACR Project GENIE).

Here’s what you will do:

  • With scientists, software developers, and product managers build and refine use cases into software requirements specifications enabling open, collaborative biomedical research.
  • Design, implement, and document tools and services including new APIs and libraries for interoperating internal and external data management systems.
  • Contribute Python object-oriented code to maintain an open-source software framework (e.g., schematic) for defining data model semantics and managing data ingress used by internal and external collaborators.
  • Use packages (such as pandas, SQLAlchemy, etc) to build tools to solve data management problems combined with Python frameworks (such as pytest) to ensure tool reliability, and Flask/Connexion to ensure interoperability.
  • Develop data validation and QC tools.
  • Follow best practices in software development, ensuring solutions can be extended and reused across multiple biomedical areas.
  • Participate in and monitor the development of external groups and communities to stay informed on best practices and standards.

We’d love to hear from you if you:

  • Have an MS in Computer Science, Bioinformatics, Computer Engineering or related computational field, or a BS and 2+ years of relevant job experience.
  • Are enthusiastic about open science, collaboration, and reproducible research.
  • Are proficient in Python.
  • Have experience working with database technologies (e.g. SQL, neo4j, etc).
  • Are proficient with collaborative development and version control systems (e.g. git).
  • Enjoy supporting diverse teams, including computational biologists, research ethicists, software engineers, product managers, and data curators, to solve complex scientific problems.
  • Have demonstrated effective verbal, written, and organizational skills with the ability to communicate with a variety of technical and non-technical collaborators.

And, also preferred, BUT not required

  • A PhD in Computer Science, Bioinformatics, Computer Engineering, or related computational field and/or 3+ years of experience in a software development role.
  • Experience developing object-oriented software design patterns (e.g. in Python or Java).
  • Understanding and architecting databases for structured and unstructured data.
  • Familiarity deploying software and infrastructure solutions to one or more widely used cloud platforms (AWS, Google, Azure).
  • Experience working with biomedical (including genomic, imaging, or clinical) data.

This is a Professional level position on our Science Professional career ladder, with a compensation range of $73,000 to 115,000. Actual compensation is dependent upon experience.

Due to Covid-19, all interviews will be conducted remotely

This position is eligible to be fully remote. Sage Bionetworks is actively working on policies and plans for the post-COVID distributed work environment.

About Sage Bionetworks

Sage Bionetworks is a nonprofit health research organization that was founded in Seattle in 2009. We use open practices that increase the reliability of scientific claims to speed the translation of science to medicine. We support responsible data sharing, objective evaluation of methods and results across researchers, and the empowerment of participants to be active partners in research. Sage is a 501c3 and is supported through a portfolio of competitive research grants, commercial partnerships, and philanthropic contributions. Sage embraces diversity, equity and inclusion. We offer a comprehensive benefits package, including relocation benefits, to bring the right talent to the team. We are based in Seattle, WA, and collaborate broadly throughout the world.

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