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    Opportunity: Computer Systems Engineer (#90847) @ Lawrence Berkeley National Laboratory -- Berkeley, CA (US)
    Submitted by Bill Cannan; posted on Wednesday, August 19, 2020

    Lawrence Berkeley National Lab's (LBNL, Joint Genome Institute (JGI, Division has an opening for a Computer Systems Engineer to join the team.


    In this exciting role, you will be responsible for the development of the Integrated Microbial Genome (IMG) systems including developing and maintaining the IMG databases, performing data loading, and helping with the development and maintenance of bioinformatics tools for genome / metagenomic annotation and analysis. You will work closely with computer scientists, biologists, and other members of the department in updating and utilizing multiple sources of biological data and participate in the analysis of microbial genomes sequenced at the JGI. You will work with internal groups, external collaborators, and members of the JGI's user community to lead development projects and troubleshoot and solve diverse and challenging problems.

    What You Will Do:
    • Participate in the IMG database design, development, and maintenance.
    • Help isolate genome and metagenome data loading.
    • Maintain and improve the IMG data loading pipelines.
    • Investigate and review new and existing data sources for IMG.
    • Work closely with JGI biologists to gather requirements, and to improve the IMG databases.
    • Use NERSC clusters to perform big data computation for the IMG database contents.
    • Work closely with IMG pipeline team and IMG User Interface (UI) team to ensure the integrity and consistency of the IMG system.
    • Provide customer support by responding to software defect reports, requests for new features, or ad hoc requests.
    • Participate in writing documentation, user guides, and IMG publications.
    • Attend weekly IMG development meetings and code review meetings.
    • Participate in collaboration with other JGI groups and KBase when requested by managers.
    • Publish in peer review journals and contribute to scientific research papers and reports.
    Additional Responsibilities as Needed:
    • Attend standing meetings with the other JGI Groups.
    • Participate in presentations and discussions about the team's work.
    • Participate in database and software release testing.
    • Lead the IMG database team and provide guidance to more junior members in the team.
    • Lead the IMG database design, development, and maintenance.
    • Manage isolate genome and metagenome data loading.
    • Lead the effort to maintain and improve the IMG data loading pipelines.
    • Investigate and review new technologies to improve the IMG databases.
    • Apply analytical skills and creativity to solve diverse and challenging problems.


    What is Required:
    • A minimum of 8 years of related experience with a Bachelor's degree; or 6 years and a Master's degree; or equivalent experience
    • Multi-year experience with multiple programming languages including perl and python
    • Multi-year experience with relational database systems such as Oracle and MySQL
    • Excellent communication skills and writing skills
    • Knowledge of public genomic data sources such as Genbank and KEGG
    • Ability to work in a collaborative environment
    • Some experience with user support
    Additional Desired Qualifications:
    • Familiar with cluster computing
    • A minimum of 12 years of related experience with a Bachelor's degree; or 8 years and a Master's degree; or equivalent experience
    • Experience and skills to lead a development team
    • Strong publication record


    • This is a full time, 1 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
    • Classification will depend upon the applicant's level of skills, knowledge, and abilities.
    • M-F, exempt (monthly paid) from overtime pay
    • Salary is commensurate with experience.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.


    Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.


    Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. To view information about the many rewards that are offered at Berkeley Lab – Click Here (


    JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest

    They say it's all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class multidisciplinary science within a diverse and respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Genome Institute (JGI) addresses the most pressing energy and environmental challenges using integrative genome science approaches. JGI takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of our next ground-breaking discoveries?

    Berkeley Lab (LBNL, addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science.


    Apply directly online at[...]84880 and follow the on-line instructions to complete the application process.


    The posting shall remain open until the position is filled.


    Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4 ([...].html). Click here ([...]t.htm) to view the poster: "Equal Employment Opportunity is the Law".

    Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers.

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