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    Opportunity: Software Developer 3/Team Lead -- Sequencing Quality Control and Analysis (#75041) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)
    Submitted by Hannah Kuhns; posted on Wednesday, August 29, 2012


    Organization: GN-Genomics

    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 to provide technical support and guidance to the Sequencing Quality Control (QC) and Analysis Team. Under general supervision, will serve as a team lead to allocate group resources, assign work to group members and manage the provision of support for existing production software systems for sequence quality control, assembly, and other standard analyses. Will be responsible for managing the design, implementation, testing, and deployment of extensions/improvements to the existing systems, including the incorporation of new techniques and algorithms for performing standardized, production-scale analyses. Will also provide hands-on software development support to the Sequencing Informatics group. Position reports to the overall Sequencing Informatics group lead and will interface with other group leads.

    The majority of duties will focus on planning, coordinating, and managing the activities of the team, with 20-30% focusing on software development.

    Specific Job Duties:
    • Plan and manage the design, implementation, testing, and deployment of extensions/improvements to the existing Quality Control and Genome Improvement systems.
    • Work closely with Bioinformatics Analysts to build and maintain automated DNA and RNA sequence analysis pipelines.
    • Manage the support of the existing production Quality Control and Analysis systems, including the resolution of custom user and data retrieval requests.
    • Follow prescribed practices for software version control, testing, and release engineering
    • Serve as technical lead and software architect of Quality Control and Analysis system.
    • Allocate QC & Analysis (Q&A) group resources and assign work to team members.
    • Assist with the planning of the migration of existing systems to third-party systems.
    • Coordinate team activities with the other Sequencing Informatics group leads, as well as the overall Sequencing Informatics group lead.
    • Gather feedback and requirements to develop software for the Sequencing Informatics group.
    • Mentor and cross-train other group members in software development and design.
    • Present technical and analytical status in weekly meetings and contribute to publications.


    • B.S. in Computer Science or a related scientific field (or equivalent experience) and a minimum of five years related experience
    • Demonstrated experience with Perl/Python and experience with database design and performance tuning in MySQL
    • Demonstrated experience leading a team of software developers in a customer service oriented environment
    • Knowledge of Molecular Biology and sequence analysis tools
    • Demonstrated success designing and implementing systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D center or automated manufacturing facility
    • 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 diverse and challenging problems
    • Effective time management, organization, and planning skills with the ability to allocate resources and assign work to meet goals and deadlines
    • Talent for working well under short deadlines and handling multiple tasks simultaneously
    • Ability to work effectively in a diverse team environment


    • Demonstrated experience with at least some of the following: MySQL, Perl/CGI, Javascript, Ruby (with Rails), Java, PL/SQL, CVS, Subversion
    • Experience developing web-based GUI
    • Experience working with lab information management systems (LIMS)
    • Experience working with bioinformatics tools and/or analysis techniques


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


    Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a safe and diverse workforce.

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