Java Software Engineer

Java Software Engineer

Position Summary

At Sage Bionetworks, we believe that we can learn more by learning from each other. By improving the way scientists collaborate, we help to make science more effective. We partner with researchers, patients, and healthcare innovators to drive collaborative data-driven science to improve health. Making science more open, collaborative, and inclusive ultimately advances biomedicine.  

The technology platform team at Sage is  developing a system called Synapse to support open data-driven biomedical research, and serve as a public resource for the scientific community. This platform has already been used to support a number of high profile scientific studies in oncology, neurodegenerative, neuropsychological, and other disease areas.  

What you’ll be doing:

The primary focus of this position is the engineering and support of the web-services/back-end tier of Synapse, our scientific collaboration platform.

  • Work with product manager and key users to understand requirements.
  • Collaborate with fellow engineers on feature design.
  • Implement new features and improve existing ones, following our engineering best-practices for code organization, documentation and testing.
  • Help analyze the performance of, optimize and ensure the continued up-time of the deployed system.

We’d love to hear from you if you have:

  • A BS or MS in Computer Science or equivalent
  • Versatile and strong programming skills:
    • Expert-level Java experience is a strict requirement for the position.  
    • Experience with Java frameworks and open source technologies, especially Spring
  • A strong understanding of object-oriented design and programming, and design patterns
  • An ability to effectively collaborate with other team members on n-tier architecture and REST API development
  • Experience building, deploying, and supporting software in production environments
  • Practical agile development lifecycle experience.  Familiarity with software development tools including Eclipse, Jira, Maven, GitHub etc.

Additional Skills/Preferences

  • Familiarity with SQL and how to structure an RDS schema for best performance
  • Familiarity with other languages used on our team, especially Python
  • Commitment to test-driven development, and rapid, automated release cycles
  • Strong verbal, written, and organizational skills
  • Self-starter with the ability to multitask and thrive in a dynamic start-up environment
  • Experience with one or more of the following:
    • SaaS architectures that leverage commercial IaaS platforms, especially Amazon Web Services
    • Bioinformatics / genomics / biomedical data and use cases
    • Open source software development

About the Team

We are an 18-person professional software engineering team embedded in a 60-person research institute with world class experts in genomics, bioinformatics, statistics, and computational biology.

We care about:

  • Providing an entrepreneurial environment and freedom to rapidly develop technological solutions to complex problems.
  • Test-driven development, continuous builds, and rapid automated deployments.
  • Intra-disciplinary collaboration, with emphasis on creating clean, well-structured code.

About Sage Bionetworks

Sage Bionetworks is a world-leading nonprofit biomedical research organization in Seattle, WA.  We are dedicated to building and supporting open communities of collaborative research in human health and genomics. We are developing multiple initiatives designed to facilitate scientific collaborations and enable direct contributions of ideas and data from citizens to research projects.

Sage embraces diversity and equity.   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.

Apply here.

Current Positions

Computational Oncology

The Computational Biology group focuses on developing integrative probabilistic models for prediction of disease phenotypes and validating of hypotheses generated by novel methodologies. Currently opportunities include: positions in Oncology focused on conducting original research in analyzing large-scale high dimensional genomics data to develop predictive models of cancer phenotypes. Positions in collaboration with the recently merged Sage/DREAM effort, focused on designing and implementing crowd-sourced collaborative challenges around cancer phenotype prediction problems. Positions in stem cell bioinformatics with a focus on development of the data and analysis bioinformatics portal for the Progenitor Cell Biology Consortium, as well as research projects on modeling molecular mechanisms underlying stem cell differentiation.

Digital Health

Sage Bionetworks’ digital health program is designed to improve disease characterization through the use of sensor-based technologies and bi-directional feedback to improve health monitoring and provide quantitative metrics to assess disease impact on health and on quality of life. We maximize the insights gained from these efforts by providing them through Synapse, a collaborative compute platform. Our mHealth team includes expertise in software engineering (both iOS and Android), clinical study design and development, data governance and data analysis. We are actively involved in projects across a range of disease areas and within the Precision Medicine Initiative.

Neurodegenerative Research

An overarching goal of the Neurodegenerative Research (NDR) group is to improve understanding of the molecular mechanisms of neurodegeneration via computational analyses of high-dimensional genomic data-sets. Our group leads analyses of such data in consortia focused on Alzheimer’s Disease (AD) and related neurodegenerative disorders, including AMP-AD and MODEL-AD. We also work across disciplines to develop technologies that make these analyses available to a wide audience of researchers. Most notably, we recently celebrated the launch of Agora, an interactive, web-based explorer that provides access to research and analyses of nascent AD drug targets produced in conjunction with the NIH-led Accelerating Medicines Partnership.

Systems Biology

The Systems Biology research group at Sage Bionetworks is working to understand the underlying mechanisms causal to common disease. We use large-scale genomic analysis to identify disease subclasses, generate diagnostic and prognostic biomarkers, and to identify pathophysiology causal to disease in collaboration with academic and industry partners. Our current portfolio is focused on neurobiology, spanning both neurodegenerative and neuropsychiatric disorders, and includes projects in other disease areas including immunology, metabolic disease and craniofacial deformation.

Technology Platforms & Services

We’re working on the tools and platforms required to gather, share and use biomedical data in novel ways. These are targeted both at the research community, as well as organizations and individuals who are involved in providing data and being involved in the research process. They range from the technology platforms Synapse and BRIDGE, through novel methods of addressing governance issues around the distribution of human data such as E-Consent, to the ability to run Challenges to solve data-driven questions through our partnership with DREAM.