Senior Software Engineer

Oregon  ‐ Onsite
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Description

Job Title: Senior Software Engineer
Department: Computational Biology Department, OHSU School of Medicine

The Computational Biology Program at Oregon Health and Science University (OHSU), Portland, OR is committed to leading the development of next-generation patient care through discoveries made by big data analytics, enabled by values of open access data, open source code, highly collaborative team science, and professional software engineering methodologies.

We are seeking a skilled software engineer with primary responsibilities of designing and building innovative software, APIs, data models and relational schemas, system integrations and automation tools to support the operations, collaborations and strategic initiatives of the Knight Diagnostic Laboratory and Knight Cancer Institute. Key skills include the ability to apply core computer science priciples in data structures and algorithms, as well as object-oriented design patterns to novel problems where no commercial solutions currently exist. This position will function within a distributed team-oriented software development environment working towards developing a distributed data / workflow management and analytics platform for genomic and clinical applications in active collaboration with leading international efforts such as the Global Alliance for Genomics and Health (GA4GH, ). A successful candidate will contribute to international development of standardized APIs and data schemas, and develop implementations compatible with such APIs, ensuring that the system is interoperable within the emerging community ecosystem of software tools.

This position will primarily work on software systems to support genomically guided cancer precision medicine, in collaboration with the Knight Diagnostic Laboratory (). Therefore, this position offers the unique opportunity to develop software tools that are used to directly impact cutting-edge patient care every day. Software, tools, and best practices applied in this clinical setting will be made available as open-source, re-runnable resources to the broader OHSU and public research community.

OHSU is ranked as one of the nation's top biomedical institutions in patient care, research, and education, with an annual operating budget of over $2.3 billion, over $340 million in annual grant funding, over 4,000 students and trainees, and nearly 1 million patient visits per year. Multiple departments rank among the top 5 in annual grant funding, including neuroscience, microbiology, ophthalmology, otolaryngology, and emergency medicine.

The Knight Cancer Institute at OHSU is an international leader in cancer research and precision treatment. The institute's director, Brian Druker, M.D., helped usher in the era of precision cancer medicine with his discovery that cancer cells could be shut down by disabling the molecules that drive their growth without harming healthy cells. The institute continues to build upon its scientific and clinical leadership; both public support and private philanthropy have provided crucial resources to advance its progress. Most recently, Dr. Druker's plans to advance the early detection of cancer inspired Nike Co-Founder Phil Knight and his wife Penny to pledge a $500 million donation if OHSU raises an additional $500 million as part of a two-year fundraising campaign. The OHSU Knight Cancer Institute is also attracting powerful research collaborations with technology leaders such as Intel Corporation and FEI Co., who want to be part of the Knight's mission to end cancer as we know it.

OHSU provides substantial resources to enable data intensive science, including a world-class exascale super computing cluster, close interactions and resource commitments by leading technology companies such as Intel, tight integration with clinical and basic research programs across campus, graduate training programs in quantitative biosciences, biostatistics, biomedical informatics, bioinformatics and computational biology, and substantial long-term resource commitments, including the $1 billion Phil and Penny Knight "challenge" to support cancer research, with a significant focus on computation.

Responsibilities
•Design and develop scalable, reliable and maintainable software using a variety of languages and frameworks (e.g. Java, Spring Framework, SQL) that integrates with relational databases.
•Develop APIs and data models for representing and querying clinical and genomics data and their associations.
•Develop ETL scripts/processes to clean/move data.
•Conduct and participate in code reviews.
•Design and build system interfaces/integrations.
•Analyze applications and systems to identify opportunities for simplification and/or enhancement.
•Prepare technical documentation based on deliverables.
•Code, conduct and document functional and performance tests. Support implemented processes, customizations, and interfaces. Help to ensure data integrity and validity of applications and databases.
•Establish and maintain standards for structured software & systems engineering, including requirements, design, code, test, quality, configuration & release management and project management.
•Mentor junior team members in developing applications.
•Contribute content to grant applications and publications derived from collaborations.
•Participate in leading international efforts, such as GA4GH, aimed at establishing best practices, standards, and APIs for genomic data representation and analysis. Work through GitHub to integrate with large-scale open source development teams.
Start date
As soon as possible
From
Oregon Health and Science University
Published at
26.02.2015
Project ID:
858452
Contract type
Freelance
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