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    Opportunity: BIOINFORMATICS Computing Consultant (#73194) @ Lawrence Berkeley National Laboratory--Berkeley, CA (US)
    Submitted by Hannah; posted on Saturday, February 04, 2012

    Submitter

    BACKGROUND

    Organization: NE-NERSC

    NERSC and the Joint Genome Institute (JGI) are searching for an individual who can help biologists exploit advanced computing platforms. JGI provides production sequencing and genomics for the Department of Energy. These activities are critical to the DOE missions in areas related to clean energy generation and environmental characterization and cleanup. JGI has recently partnered with NERSC, the DOE Office of Science's flagship computing center, a world leader in providing high-performance computing tools and expertise that enable computational science of scale. This partnership gives JGI staff access to supercomputer class systems, advanced architectures, and large-scale storage systems enabling JGI to address the most demanding genomic problems. This position will help bridge the gap from biology to computational science. The position will support the JGI mission by directly engaging with biologists to assist them with effectively using the range of computational resources at their disposal.

    RESPONSIBILITIES

    Computer Systems Engineer 2:
    The individual is expected to provide assistance on how to architect and implement genomic applications that would include porting or modifying existing pipelines to run on new architectures and platforms including HPC systems and Cloud computing systems. This includes investigating and developing new more efficient and scalable algorithms that can handle the growing volume of genomic data. In addition, the individual will have the opportunity to explore new computing models such as Hadoop, HBase, and accelerators to understand how they can be used to address challenges for the JGI. The individual will serve as the main point of contact between JGI and NERSC, assessing user requirements and communicating user scientific and computing needs to both organizations. The successful candidate will help educate and train users by creating content for the NERSC website with online tutorials and documentation, giving presentations, and attending conferences and will communicate with users about new opportunities and capabilities in software and systems and advise them in effectively transitioning to new technologies.

    Computer Systems Engineer 3:
    In addition to the duties of the CSE 2, the CSE 3 will take a lead role in at least one of the activities described above, take responsibility for managing and solving complex problems, have frequent interactions with users to provide technical guidance, participate in setting direction for future user activities and participate in collaborations with research scientists.

    REQUIREMENTS

    Computer Systems Engineer 2:
    • Bachelor's degree in a science or a computer science discipline or equivalent experience and a minimum of 4 years related experience
    • Demonstrated ability to work independently, work collaboratively in an interdisciplinary team, and contribute to an active intellectual environment
    • Experience with a variety of bioinformatics tools (assemblers, comparative analysis tools, phylo-genetic, etc.)
    • Broad computational background including knowledge of Linux, C, C++, Perl, and Python
    • Ability to work effectively with scientists understanding user needs, showing initiative, tact and judgment developing solutions
    • Excellent written and oral communication skills
    Computer Systems Engineer 3:
    In addition to the above requirements for a CSE 2, the CSE 3 must have a minimum of 8 years related experience. The CSE 3 must have a demonstrated ability to assume a leadership role, ability to grasp complex problems and develop solutions, and possess in-depth background in bioinformatics tools.

    PREFERENCES

    • An advanced degree in computational science, computer science, or bioinformatics
    • Familiarity with high-performance computing (including MPI , novel architectures (accelerator, FPGA, etc) or cloud computing
    • Familiarity with emerging distributed computing models such as Hadoop
    • Experience supporting and deploying bioinformatics pipelines

    TERMS

    Note: This is a one year term, renewable each year, with the possibility for conversion to an indefinite (career) appointment based on satisfactory job performance, availability of funds and ongoing operational needs.

    HOW TO APPLY

    Apply directly online at http://bit.ly/lbl7[...]atics and follow the instructions to complete the application process.

    POLICY

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

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