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    Opportunity: Software Developer 3 -- Integrated Fungal Genomics (#79510) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)
    Submitted by Hannah Kuhns; posted on Monday, June 30, 2014


    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an opportunity for a skilled and creative bioinformatics software developer to develop MycoCosm (, the integrated fungal genomics resource. MycoCosm combines visualization and analysis tools, provides users with access to JGI and non-JGI fungal genomics data. With expected dramatic expansion of genomics data due to significantly increase genome sequencing, MycoCosm requires development of a wide range of new front end and backend features for easy use and high performance. We are looking for JAVA/JavaScript software developer with technical expertise in developing web applications and relational databases, experienced in the bioinformatics domain.


    Specific Job Duties:
    • Work as part of the team that develops and supports MycoCosm (, a web portal and data system for fungal comparative genomics.
    • Design and develop software for the MycoCosm/Fungal Program.
    • Design effective solutions compatible with existing systems.
    • Interface with end-users to gather feedback and requirements.
    • Provide daily client support, including occasional evening and weekends.
    • Participate in system architectural review and design.
    • Observe and promote configuration management and deployment policies.
    • Participate in formal and informal design and code reviews.
    • Apply analytical skills and creativity to troubleshoot problems of diverse scope.
    • Monitor web statistics, determine MycoCosm usage patterns.
    • Create documentation and training materials


    Key Success Factors:
    • Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of five years of work experience.
    • Demonstrated success designing, implementing, and supporting large complex systems and software in a scientific or technical environment.
    • Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
    • Experience with genomics data, analytical tools and methods
    • Demonstrated experience coding and debugging Java and object-oriented Perl.
    • Expertise with web development: HTML, CSS and Javascript
    • Strong SQL skills, with good knowledge of database performance optimization related to schema design
    • Excellent analytical, problem-solving and decision-making skills to independently make sound judgments and creative solutions to complex problems.
    • Effective time management, organization and planning skills; ability to work effectively in team environment.
    • Ability to apply analytical skills and creativity to solve diverse and challenging problems.
    • Good software development practices – self-documenting code, source control, bug tracking.
    • Experience with SGE or other HPC environments.
    • Experience with large MySQL-based data sets.


    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.

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