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    Opportunity: Software Developer (#90882) @ 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.

    The Software Developer will lead the design and development of software in support of synthetic biology projects. The successful candidate will develop and evaluate software for gene or pathway construct design and DNA sequence data analyses. The developer will interact closely with all members of the DNA Synthesis group to design, test, and implement computational tools to streamline the high-throughput design and assembly of synthetic DNA enabling the deployment of cutting-edge molecular approaches at scale. The Software Developer will also be responsible for assessing the utility of existing synthetic design tools, improving them according to the project needs, integrating with existing tools (if appropriate), and adding user interfaces for general use by internal and external users.

    What You Will Do:
    • Lead and/or participate in the development of computational approaches to aid in the design, assembly and analysis of DNA constructs, oligonucleotide pools and synthetic libraries.
    • Work closely with the platform group to provide interpretation of downstream data output and iteratively improve design software accordingly.
    • Maintain an accurate and detailed record of tools developed.
    • Ensure that developed tools have biologist-appropriate user interfaces and functionality.
    • Present technical and analytical status updates in weekly meetings.
    • Contribute to scientific research papers, reports and presentations.
    • Follow standard practices for executing version control, testing, and release.
    • Implement data-specific user interfaces and data retrieval reports.
    • Assist users to resolve tool malfunction or data entry errors.
    • Survey and provide feedback on existing and new third-party software that can be incorporated into our workflows.
    Additional Responsibilities as Needed:
    • Stay up to date with new DNA assembly and gene/genome editing technologies.
    • Train biologists to use the tools being developed.


    What is Required:
    • A minimum of 5 years of related experience with a Bachelor's degree; or 3 years and a Master's degree in Computer Science, Bioinformatics, or related field; or equivalent work experience
    • Experience writing software for molecular or synthetic biology applications
    • Experience with web application frameworks (Tomcat/Django/Flask)
    • Experience with relational database structure and management (SQL, Postgres, MySQL)
    • Experience with HPC environments
    • Experience with containers (Docker)
    • Experience with and adherence to software development best practices (version control, code review)
    • Proficiency with scripted programming languages (Python preferable) in a Unix environment
    • Proficiency with object-orientated languages (JAVA preferable)
    • Demonstrated proficiency in utilizing assembled genomes, various alignment tools, visualization tools, and other genome interrogation and analysis software.
    • Analytical skills sufficient to troubleshoot discrepancies in data results and make improvement recommendations
    • Strong organizational and record-keeping skills
    • Effective oral and written communication skills as well as interpersonal skills
    • Ability to work independently and as a team member in a diverse team environment
    • Ability to handle multiple tasks in parallel while working on a large number of projects
    Additional Desired Qualifications:
    • Experience in writing software for analysis of DNA sequence or experimental data
    • Experience with web development and related technologies (Javascript, ORMs)
    • Experience with full stack software development and deployment
    • Knowledge of general molecular biology techniques and the laboratory DNA sequencing technologies and genetics, or related field or equivalent experience preferred
    • Familiarity with commercial laboratory software (e.g. Benchling, LabKey etc)
    • Familiarity with statistical tools and interpretation of data
    • Proficiency with compiled programming languages (C/C++, Java or others) in a Unix environment


    • This is a full time career appointment.
    • Classification will depend upon the applicant's level of skills, knowledge, and abilities,
    • 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: 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[...]84881 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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