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    Opportunity: Software Developer - Kbase (#73653) @ Lawrence Berkeley National Laboratory--Berkeley, CA (US)
    Submitted by Jeff Todd; posted on Tuesday, May 08, 2012


    Organization: PB-Physical Biosciences


    The U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) project is building the next generation computational resource for biological investigation. This innovative software system will change the way biological research is done, creating the "go-to" online community for biological research and providing tools for systems biology experimental design and data analysis, creating a platform to enable predictive modeling and hypothesis generation and testing.

    Strong collaborations with other DOE projects, including biofuel research, bioremediation, and research into the biological role in the Earth's carbon cycle will provide exciting opportunities for advancing fundamental and applied biological science, providing a deeper understanding of how Nature works. Software development will cover the full spectrum of technologies, from advanced user interface design, data integration, database and software interface design, and high performance computing and bioinformatic algorithm development.

    Work will be performed at Lawrence Berkeley National Laboratory, a national lab that offers a research environment similar to academic institutions with a reasonable work/life balance, working with a talented team with diverse experience and offering many opportunities to broaden one's knowledge and interact with scientists on other breakthrough projects that will help shape the future.

    The Software Developer will work collaboratively but 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. Classification will be at the 2, 3 or 4 level depending upon the applicant's level of skills, knowledge and relevant experience.


    • Plan, organize, prioritize and complete assigned tasks and projects in a timely manner. Frequently and clearly communicate tasks or project status to collaborators and customers to either set or negotiate expectations.
    Level 2 job duties include:
    • Work with other KBase project members to plan and implement User Interfaces, APIs, and Data Standards for linking core resources and databases in the KBase.
    • Work closely with users of the analysis software to ensure that their needs are being met. Work with users to test and debug applications. Prepare presentations and papers for internal use, conferences, and peer-reviewed publication. Maintain accurate documentation and source-code control for all work-product.
    Level 3 job duties include:
    • Play the lead role and make sound judgments while coordinating with the PI and other members of group in designing, developing, and distributing software for genomic analysis, systems biology analysis including metabolism, analysis of microbial community structure and function, and sophisticated data analysis leveraging such tools as the MicrobesOnline, metaMicrobesOnline, and GLAMM websites and databases. Define software requirements and take a lead role in determining the week-to-week direction of the work. Identify problems and recommend viable solutions to software and data management issues.
    Level 4 job duties include:
    • Providing supervision and training to other members of the group. Provide leadership and guidance for motivating/coordinating developers to adhere to standards, integrate their projects, and develop towards stakeholder needs including demonstrations for DOE and the community, and solving scientific problems of stakeholders. Participate in the recruitment, hiring, and performance evaluation of a variety of scientific, technical and professional staff.


    Key Success Factors:
    • Essential Qualifications for all levels: Demonstrated skills, knowledge and work experience in engineering, computer science, and biology especially in regard to functional and/or comparative genomics, microbial ecology, genetic networks, metabolic engineering, systems biology, and/or synthetic biology
    • Demonstrated experience with problem solving in computational biology
    • Experience in bioinformatics software design and engineering, mathematical analysis and comparative and functional genomics
    • Experience with developing applications to display/visualize scientific (preferably biological) data
    • Experience with a code management system, preferably CVS or SVN
    • Must posses both high analytical skills and programming skills (language unspecified but prefer C, C++, or Java and Perl or Python), when working with projects of moderate scope where data requires a review of identifiable factors.
    • Ability to creatively work with problems in comparative and functional microbial genomics and network biology, exercising judgment within defined procedures and practices to determine appropriate action
    • Effective interpersonal, verbal and written communication skills with ability to accomplish goals as a team member
    • Ability to collaborate with a team of scientists
    • Demonstrated ability to work collaboratively with programmers, engineers, post-docs, graduate students, and undergraduates from diverse backgrounds
    • Must have ability to handle multiple projects and tasks
    Software Developer 2 qualifications:
    • Bachelor's degree or equivalent experience and a minimum of 2 years related experience
    Software Developer 3 qualifications:
    • Five years of experience developing software in a research or technical filed or for scientific applications
    Software Developer 4 qualifications:
    • Bachelor's degree or equivalent experience and a minimum of 8 years experience developing software in a research or technical field or for scientific applications


    Additional desired qualifications:
    • Masters degree or higher (PhD preferred) in computational biology, microbiology and bio- or chemical engineering discipline
    • Familiarity with online public sequence and microbiology databases
    • Familiarity with genome sequence data and analysis
    • Familiarity with metabolic pathways and enzymology
    • Coursework in microbiology, genetics or general biology
    • Experience with tools such as Matlab and Mathematica
    • GUI design and usability testing experience is a plus.
    • Familiarity with AJAX and javascript or other dynamic, interactive web based applications
    • Familiarity with concepts inherent in developing data standards
    • Experience writing shell scripts


    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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