Senior Research Assistant

Posted on by Micaela Brun
Job ID: 1669243735
Job date: 2017-11-14
End Date:

Company : Oregon Health & Science University 

Country :

Role : Research Scientist 


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Job Description:
OHSU, Portland, OR has an opening for Senior Research Assistant in Computational Biomedicine. The Research Assistant will participate in the Galaxy project (http://galaxyproject.org), which builds open­ source software to enable large­scale computational medicine and genomics analyses. Galaxy is used by thousands of investigators across the world. Primary projects that the research assistant will contribute to include federated storage and compute for high­throughput genomics datasets in Galaxy and improving its framework for querying the data and metadata of both local and distributed high­throughput sequencing datasets. Particular areas of work will include (a) development of a massively parallel framework for indexing, persisting, and retrieval for the large scale genomic datasets on distributed relational and NoSQL databases; (b) querying high­throughput genomics data for interactive visualization and analytics; (c) similarity search engine for genomics datasets; and (d) distributed storage and compute of high­ throughput genomics data across multiple computing clouds.

Responsibilities:

Using the skills and education required below:

  • Pursue research complementary to the lab's themes in computational biomedical science;
  • Develop open­source software for computational biomedicine and genomics.

Job Requirements

Requirements:

  • BS in computer science or information technology.
  • Must have the following skills which may be gained either as part of post-baccalaureate education or work experience:
    1. Cloud computing, specifically use of virtualization for distributing data storage and compute;
    2. NoSQL databases and relational databases;
    3. Information retrieval approaches (e.g., TF­IDF, PageRank) multi­dimensional and multi­resolution data structures;
    4. Multi­resolution indexes for high­throughput genomics data;
    5. High­level query languages for high­throughput genomics data (e.g., GEMINI, GMQL); similarity search and correlation assessment for high­throughput genomics data;
    6. Software engineering in a team environment contributing to a large, shared open­source project;
    7. C# .NET, Java, or C++ and Python
    8. Developing bioinformatics pipelines for analysis of high­throughput genomic data using open­source bioinformatics tools such as SAMtools, BAMtools, Galaxy, MACS, IGV, IGB, and UCSC Genome Browser
    9. Programming experience on Galaxy codebase (https://github.com/galaxyproject/galaxy).
    10. Expertise in algorithms/methods for performing large computing tasks across heterogeneous computing clouds/resources to optimize various criteria, such as minimal data transfer or cost or maximizing utilization of available computing resources (example methods include genetic algorithms, binning and profiling, and using Probability Density Function (PDF)-optimized scalar quantization to distribute data).

    Requeriments :

    Skills :

    Areas :

    Additional Info:
    Please email CV to Holly Chung at chunho@ohsu.edu or by mail to Holly Chung, Mail Code L333, OHSU, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239.

    Oregon Health & Science University values a diverse and culturally competent workforce. We are proud of our commitment to being an equal opportunity, affirmative action organization that does not discriminate against applicants on the basis of any protected class status, including disability status and protected veteran status. Individuals with diverse backgrounds and those who promote diversity and a culture of inclusion are encouraged to apply. To request reasonable accommodation contact the Affirmative Action and Equal Opportunity Department at 503-494-5148 or aaeo@ohsu.edu.

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