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    Opportunity: Bioinformatics Pipelines Software Engineer (#87563) @ Lawrence Berkeley National Laboratory -- Walnut Creek, CA (US)
    Submitted by Bill Cannan; posted on Saturday, June 29, 2019


    The Joint Genome Institute (JGI) within Berkeley Lab has an exciting career opportunity available for a microbiome researcher with an interest/experience in data pipeline development and portability. The Department of Energy is funding a pilot program, the "National Microbiome Data Collaborative" (NMDC) which aims to address many of the pressing issues in microbiome research, including data integration, making data FAIR (findable, accessible, interoperable, and reusable) and establishing standardized workflows for data processing.

    In this role the NMDC software engineer will work closely with JGI's IMG group and collaborate with a diverse set of engineers and scientists, to port and standardize IMG's annotation pipelines through a workflow language (e.g. CWL) and incorporate them into standalone software packages (e.g. Docker containers) that can be freely obtained and run in any environment.

    This position is within the IMG Pipelines Group and will report to the IMG Pipelines Group team lead at the Joint Genome Institute in Berkeley, CA.

    Classification will depend upon the applicant's level of skills, knowledge, and abilities. This position will be filled at the Computer Systems Engineer 2 or Computer Systems Engineer 3 level, dependent on experience.


    What You Will Do (Computer Systems Engineer – Level 2):
    • Work on porting and standardizing portable and scalable data pipelines.
    • Ensure accurate software version control, testing and release engineering.
    • Create documentation and training materials.
    • Serve as a key contributor called upon to troubleshoot and recommend solutions to technical problems.
    Additional Responsibilities as needed (Computer Systems Engineer – Level 2):
    • Present to audiences within and outside the lab.
    • Assist with the curation and processing of legacy and current data and metadata.
    In addition to the above, the Computer Systems Engineer 3 responsibilities include:
    • Work on complex issues where analysis of situations or data requires an in-depth evaluation of variable factors. Exercise judgment in selecting methods and techniques to improve genomic analysis within the IMG Pipelines.
    • Take a lead role in analyzing and evaluating varied factors in produced predictions, perform manual curation and large-scale computational analysis of predicted gene models and annotations.
    • Take a lead role in developing processes/procedures and providing and improving protocols, methods and tools for genome annotation and analysis.
    • Lead the efforts to proactively look for additional opportunities to make contributions to the IMG Pipelines.
    • Networks with key contacts outside of JGI.


    Minimum Qualifications for Computer Systems Engineer – Level 2:
    • Bachelor's degree in Computer Science, Engineering, Bioinformatics, or a related field with a minimum of 5 years of work experience, or an equivalent combination of education and experience.
    • Demonstrated experience with the entire software development process, from requirements through design to implementation and deployment.
    • Proficiency programming in Python.
    • Experience in creating workflows via a workflow language.
    • Experience in the containerization of applications (e.g. via Docker).
    • Experience with CI/CD tools and frameworks (e.g., Gitlab, Jenkins).
    • Experience with modern cluster/cloud/distributed computational and storage systems.
    • Experience applying modern software technologies for databases, RESTful services, computational workflows, data processing pipelines, and/or scientific reproducibility.
    • Working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
    • Familiarity with SQL and relational databases such as Oracle, MySQL or Postgres.
    • Ability to conduct analysis and work independently.
    • Excellent English written and oral communication.
    • Strong interpersonal skills for working in a diverse team environment.
    In addition to the above, the Computer Systems Engineer 3 qualifications include:
    • Minimum of 8 years of related experience with a Bachelor's degree; or 6 years and a Master's degree; or equivalent experience.
    • Excellent track record of success in previous employment.
    Additional desired qualifications for Computer Systems Engineer – Level 2:
    • Master's degree or equivalent work experience.
    • Demonstrated experience working in similar fields.
    • Familiarity with different types of sequence data.
    • Demonstrated experience working in high-performance computing.
    Desired qualifications for the Computer Systems Engineer 3:
    • Experience with genomic analysis software, and knowledge of various bioinformatics algorithms related to sequence analysis.
    • Ability to provide creative and in-depth solutions to pipeline or analysis issues encountered at work.
    • Ability to suggest, design and implement new, useful features to improve the IMG Pipelines.
    • Ability to constantly keeping up with technology changes in the field.


    • This is a full time, 2 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. This position will be filled at the Computer Systems Engineer 2 or Computer Systems Engineer 3 level, dependent on experience.
    • Full-time, M-F, exempt (monthly paid) from overtime pay.
    • 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 JGI/Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.


    Salary is commensurate with experience.

    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 employee 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 science within a diverse, 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 Institute (JGI) addresses the most pressing energy and environmental challenges. This summer, 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 the next ground-breaking discoveries in the public interest?

    The JGI is comprised of highly-skilled and diverse talent founded on a culture of scientific excellence, trust, curiosity, passion, and collaboration.

    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[...]64254 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.pdf) to view the poster: "Equal Employment Opportunity is the Law".

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