Description
Job Title:Scientific Programmer
Department: Computational Biology Deparment, 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 scientific programmer to develop genomic, imaging, and clinical analysis applications on a distributed data / workflow management and analytics platform currently under development. This position will work in a team oriented software development environment, following best practices such as code sharing through GitHub and development of structured software APIs. A successful candidate will contribute to the 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.
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
•Develop custom analytics and data management applications to facilitate one or more of the following: large-scale genomic data analysis; machine learning methods to infer genotype-to-phenotype predictive models; analysis of quantitative imaging data.
•Work with the platform development team to implement scalable cloud-enabled workflows to disseminate analytical advances to the research community.
•Establish and maintain standards for structured software & systems engineering, including requirements, design, code, test, quality, configuration & release management and project management.
•Provide documentation and user support allowing computational researchers across campus to access and re-use analysis tools.
•Maintain well-curated, highly structured, transparent omics, imaging, or clinical data resources.
•Develop tools to integrate commonly used open source bioinformatics software applications.
•Participate in leading international efforts aimed at establishing best practices and standards for genomic data representation and analysis.