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    Opportunity: Informatics Software Developer (JBEI) (#76499) @ Lawrence Berkeley National Laboratory -- Berkeley, CA (US)
    Submitted by Jeff Todd; posted on Thursday, October 31, 2013



    The Joint BioEnergy Institute (JBEI) is a San Francisco Bay Area scientific partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab). JBEI's primary scientific mission is to advance the development of the next generation of biofuels - liquid fuels derived from the solar energy stored in plant biomass.

    The Software Developer will develop and maintain innovative systems to manage metabolic pathway engineering data to support JBEI's advanced biofuels research. The Experiment Data Depot is a unique application that simplifies data collection for agile research, with sophisticated tools allowing easy comparison of diverse data sets across engineered strains. The Software Developer will interact heavily with JBEI's Laboratory Information Management System (LIMS), Electronic Lab Notebooks (ELN), and bio-engineering tools like GD-ICE ( and GLAMM ( The developer will collaborate extensively with lab personnel to understand the unique aspects of the workflows, and will implement new features to facilitate their work, while also addressing higher-level data mining requirements.

    We will consider candidates at either the Software Developer 2 or 3 level depending upon the level of experience, including skills, knowledge and abilities.


    • Maintain existing code base, and add new features to JavaScript/Perl-based web application
    • Integrate application with other (primarily Java-based) systems
    • Meet regularly with scientists and postdoctoral researchers, and lab personnel to develop a deep understanding of their environment and needs
    • Develop creative (often non-technical) solutions to unique problems.
    • Provide bug fixes, new functionality, and documentation of existing Java based web apps
    • Work with researchers to automate laboratory workflows and data collection
    • Work collaboratively in a small, agile development team
    • Provide tier-2 technical support to users of data management systems.
    In addition to the duties listed above the Software Developer 3 will also perform the following duties:
    • Design and develop new software systems from the ground up
    • Serve as technical lead on development projects
    • Design and optimization of database schemas
    • Work independently with little supervision, while delivering high quality products
    • Develop high-level software QA strategies
    • Participate in inter-departmental data management strategy planning


    • Bachelor's or Master's degree (or the equivalent experience) in Computer Science or a physical science discipline
    • 3+ years of experience developing data-management software, preferably developing software for sample identification and tracking in a laboratory setting
    • Excellent programming skills (Javascript, Perl, Java, C++)
    • Demonstrate a flexible approach to software that balances technical innovation with usability, adhering to specifications developed by others (e.g., management, researchers, and other software developers)
    • Strong scripting skills (Python, Perl)
    • Familiarity with databases and SQL query-writing
    • Familiarity with source control systems (e.g. Subversion)
    • Experience developing software with Eclipse
    • Familiarity with Maven to build applications
    • Experience building reports using SQL and tools like Jasper Reports or Crystal Reports
    In addition to the above qualifications the requirements for a Software Developer 3 include:
    • 6+ years of experience developing data-management software, preferably developing software for sample identification and tracking in a laboratory setting
    • Database schema design and optimization (preferably Postgres)


    This is a one-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.


    Berkeley, CA




    For full consideration, follow the link to the job posting and apply directly to Berkeley Lab. As part of the online application process, please complete a profile, including uploading attachments relevant to the opportunity. Be sure to reference where you found the position (Bioinformatics.Org).[...]76499


    Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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