Not logged in
  • Log in
    Membership (40081+) Group hosting [?] Wiki
    Franklin Award

    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    All information groups
    Online databases Online analysis tools Online education tools More tools

    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • Career Center - Message forums

    Opportunity: Software Developer 3 -- Genome Portal and Sequence Data Management (#78957) @ DOE Joint Genome Institute -- Walnut Creek, CA
    Submitted by Hannah Kuhns; posted on Tuesday, June 03, 2014


    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting Software Developer position available in the Sequence Data Management and Genome Portal groups.
    • Produce and manage the sequence data from next-generation sequencers that supports genomic and bio-energy research science across the world
    • Work with large scale data and with large scale pipeline and processing problems
    • Work with petabyte range file and tape systems
    • Have access to some of the fastest computers in the world for computationally intensive projects
    Position will work with both the Genome Portal and Sequence Data Management Groups. Primary work will support the implementation of of data exchange between JGI and KBase. Secondary work will involve working with petabytes of data and metadata to facilitate finding and sharing of data, and in making these data available to researchers via the JGI Genome Portal.

    Specific Job Duties:
    • Develop and maintain KBase facing Genome Portal UI code.
    • Help maintain the software systems that support the data transfer between JGI and KBase.
    • Will be responsible for the design, implementation, testing, and deployment of extensions to JGI's high-throughput data management systems.
    • Will be responsible for developing customer facing web pages.
    • Analyze the impact of process, hardware or software changes on production line performance.
    • Implement sequence data management-specific user interfaces and reports.
    • Follow prescribed practices for software version control, testing, and release engineering.
    • Communicate regularly with customers and supervisory staff about plans, designs, and progress.
    • Provide status updates in regular team meetings, and coordinate development work with other members of the Sequence Data Management team and (when appropriate) Sequencing Informatics group.
    • Provide responsive support for new and existing sequence data management systems, including: prompt resolution of processing errors, software bugs, as well as resolution of custom user and data retrieval requests.
    • Troubleshoot complex systems and data management problems.
    • Other duties as assigned.


    • B.S. in Computer Science or a related scientific or technical field (or equivalent experience) and a minimum of five years related experience.
    • Demonstrated experience with one or more of the following programming languages: Python, Java, JavaScript.
    • Demonstrated experience with database programming and interfaces, preferably in MySQL or Oracle.
    • Demonstrated experience with Linux or Unix.
    • Experience developing web user interfaces.
    • Full life-cycle software development experience with the ability to work with scientific and administrative customers to define needs and priorities.
    • Ability to apply analytical skills and creativity to solve complex software and data management problems.
    • Effective time management, organization, and planning skills.
    • Talent for working well under short deadlines and handling multiple tasks simultaneously.
    • Ability to work effectively in a diverse team environment.


    • Demonstrated experience with the following: Python, JavaScript, Git/Bitbucket
    • Demonstrated experience in providing support for production software systems.
    • Experience with high performance, parallel computing, and/or grid engines.
    • Experience with Agile and Test Driven development methodologies.
    • Experience with designing and utilizing RESTful services.
    • Demonstrated expertise creating systems and software for processing large volumes of data.


    This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA. Job may require occasional travel, weekend, and after-hours work. Detailed information about the Joint Genome Institute program can be found on the World Wide Web at the following location:


    Apply directly online at and follow the on-line instructions to complete the application process.

    Organization: GN-Genomics


    Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status.

    Expanded view | Monitor forum | Save place

    Start a new thread:
    You have to be logged in to post a reply.


    Copyright © 2018 · Scilico, LLC