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22 Aug 2015

Full-Time Scientific Programmer (@ Portland)

Oregon Health & Science University – Posted by takabaya Portland, Oregon, United States

Job Description

Scientific Programmer

The Position
As an Oregon Health & Science University (OHSU) Scientific Programmer specializing in genomic, imaging, and clinical analysis applications, you will leverage your talents to change the world and contribute to the elimination of human disease. You are passionate about open-source software and transparent sharing of information. You are enthusiastic about working in a team that finds quantitative insights in complex data and develops interactive tools to enable clinicians and researchers to understand cancer. You have strong experience in thinking analytically and developing software tools.
This position will work in a team-oriented software development environment that’s committed to transparency and open-source software. The position comes with creative freedom to solve a variety of computational challenges, such as:
  • Supporting genomic analysis in R and Python.
  • Developing web-based data visualizations using libraries such as Angular and React.
  • Developing API-friendly web services in Python or Ruby to manage computational workflows.
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.
Responsibilities
We are looking for a variety of skill sets that would apply to one of more of the following:
  • 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.
Requirements
We welcome candidates with doctorate or master’s degrees in computational biology, computer science, or related technical disciplines. Candidates with bachelor’s degrees and significant accomplishments in real-world work experience will also be considered. Candidates will be hired at the appropriate position rank (e.g. research associate or senior research associate) and pay-scale based on education level and work experience. Academic appointments at the research assistant professor level may also be available for qualified candidates.
The candidate must have a desire to change the world and contribute to the elimination of human disease along with the following:
  • Advanced skills in a high level programming language, preferably Python and/or R.
  • Experience in developing scientific computing tools, preferably for one of the following domains:
  • Analysis of next-generation DNA or RNA sequencing data.
  • Advanced machine learning or statistical techniques, such as probabilistic graphical models, Bayesian inference, and optimization methods.
  • Image processing algorithms and biomedical image analysis workflows.
  • A passion for developing web services for science applications, preferably including:
  • Distributed workflow execution and data processing
  • UI design for data exploration and visualization
  • Hands-on DevOps experience for scientific computing environments
  • Strong ability to initiate and collaboratively drive projects as a dedicated and passionate member of a diverse non-hierarchical team
  • Agile selection and prioritization of tasks.
  • Ability to effectively translate and convey expertise across domains.
  • Excellent communication, analytical and organizational skills, both written and verbal.
  • Collaborative approach to resolving problems.
Preferred
  • At least three years of experience with distributed file systems, such as Lustre, and working with “big data”.
  • Masters or doctorate degree preferred.
  • High performance computing experience in a Unix/Linux environment.
  • For image analysis, familiarity with commonly used tools such as Slicer or CellProfiler.
  • Experience in a professional, team-oriented software development environment.
About OHSU
A passion for open-access innovation.
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. OHSU is one of the nation’s fastest growing biomedical institutions, bolstered by long-term resource commitments, such as the $1 billion Phil and Penny Knight “challenge” to support research in OHSU’s Knight Cancer Institute, led by Dr. Brian Druker, who pioneered the concept of gene targeted therapy by demonstrating the efficacy of the revolutionary cancer drug Gleevec in chronic myelogenous leukemia. OHSU provides substantial resources to enable data intensive science, including a world-class exascale supercomputing 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. 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.

How to Apply

Please submit your resume/CV to compbio@ohsu.edu for the initial screening.  

Job Categories: Researcher/Academic. Job Types: Full-Time.

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