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    Opportunity: Software Developer (2 or 3) - Fuel Synthesis (#74127) @ Lawrence Berkeley National Laboratory--Berkeley, CA (US)
    Submitted by Jeff Todd; posted on Tuesday, February 07, 2012



    Organization: PB-Physical Biosciences

    The Software Developer is responsible for working in a team on the creation, elaboration and maintenance of innovative software systems to aid in systems biology experimental design and data analysis at the Joint BioEnergy Institute's (JBEI) Fuel Synthesis Division. The incumbent will work collaboratively with software developers and researchers from the Informatics department and UC Berkeley, but must also show independence and leadership in research and development. The incumbent shall also be expected to present work, keep a record of activities and aid in publication of papers and writing grants.

    This will be filled as either a Software Developer level 2 or 3 depending upon several factors, including level of experience.

    Specific Responsibilities:
    • Develop new web applications for visualizing and managing data.
    • Provide new functionality and bug fixes of existing web apps such as MicrobesOnline ( and Genome-Linked Application for Metabolic Maps (GLAMM).
    • Work with researchers with in developing and maintaining a computational workflow which integrates new as well as existing tools with the final goal of enabling them to perform all tasks needed for `omics data analysis from data retrieval to visualization.
    • Work collaboratively in a small, agile development team.
    • Prepare presentations and papers for internal use, conferences, and peer-reviewed publication. Maintain accurate documentation and source-code control for all work-product.
    In addition to the duties listed above for a Software Developer 2, the Software Developer 3 will also perform the following required duties:
    • Work independently with little supervision, while delivering high quality products.
    • Serve as technical lead and overall coordinator on development projects.
    • Define software requirements and take a lead role in determining the week to week direction of the work.
    • Design and optimization of database schemas.
    • Develop high-level software QA strategies.
    • Provide supervision and training to other members of the group. Participate in the recruitment, hiring, and performance evaluation of a variety of scientific, technical and professional staff.


    Key Success Factors:
    • Bachelor's or master's degree (or the equivalent experience) in computer science or a physical science discipline
    • 2 years of experience developing data-management software, preferably in a laboratory setting
    • Able to work in a collaborative and agile environment and have excellent communication skills
    • Have a customer-oriented approach to software development and support, and be able to work directly with users
    • Experience programming with Java, C++, or C#
    • Scripting (Python, Groovy or Perl)
    • Familiarity with Unix, Linux, Windows and Mac operating systems in a development environment
    • Familiarity with databases and SQL query-writing
    • Familiarity with source control systems (e.g. Subversion or git)
    • Have 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)
    In addition to the above qualifications for a Software Developer 2, the requirements for a Software Developer 3 include:
    • 5+ years of experience developing data-management software, preferably in a laboratory setting
    • J2EE server/client application design
    • Implementing web services APIs (REST, SOAP)
    • Javascript/JQuery web client development
    • Database schema design and function writing (preferably Postgres)


    Additional desired qualifications:
    • Experience interacting with laboratory researchers to understand data management procedures and requirements and troubleshooting software problems
    • Experience developing production software in a research or technical (preferably biological) field or for scientific applications
    • Masters degree or higher (PhD preferred) in a computational biology, microbiology and bio- or chemical engineering discipline
    • Familiarity with on-line public sequence and microbiology databases
    • Familiarity with metabolic pathways and enzymology
    • Coursework in microbiology, genetics or general biology
    • Experience with developing applications to analyze and/or display/visualize scientific (preferably biological) data
    • GUI design and usability testing experience
    • Familiarity with AJAX and dynamic, interactive web based applications


    Apply directly online at[...]atics and follow the instructions to complete the application process.


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

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