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    Opportunity: Software Developer 3 -- Project Lead (Berkeley Bioinformatics Open-Source Projects) (#79548) @ DOE JGI -- Walnut Creek, CA (US)
    Submitted by Hannah Kuhns; posted on Tuesday, July 22, 2014


    The Department of Energy (DOE) Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory has an exciting opportunity available for an experienced Software Developer/Engineer 3 (Project Lead).

    This is not your typical programming job. This job requires imagination, technical savvy, drive, and a vision of bringing the latest developments in the software industry to bear on the challenges of medical diagnosis, systems biology, and biodiversity. There are large untapped opportunities in the ongoing explosion of molecular data. This position calls for an individual who can see potential connections between the latest developments in software technology and the challenges of biology, and use these insights to produce robust, flexible software that empowers researchers in the biological sciences. This experience will uniquely position the successful candidate in the emerging computational genomics job market.

    The Berkeley Bioinformatics Open-Source Projects (BBOP) is a small group of energetic individuals who are dedicated to developing tools and applying computational technologies to address fundamental biological research needs. Since 2003 BBOP has been supported by NIH research grants to innovate and build advanced data management and analysis technologies. Currently senior team members are Principal Investigators for the Gene Ontology Consortium (gene function and evolution), the Monarch Initiative (genotype to phenotype analysis), and the Apollo project (collaborative genome annotation). Everyone on the team is motivated to advance research by pioneering effective new strategies that can meet the many challenges of biological data management, representation, visualization and analysis. The group is highly collaborative and travel frequently to work with a global network of diverse investigators.

    BBOP is seeking an experienced software engineer with proficiency in technical project leadership ability. The position will contribute to building an infrastructure that providing an ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in the context of genetic and genomic data, using semantics and statistics.


    The primary role will be developing and extending web-based genomics and functional collaborative annotation environments. These include: Apollo, a web based genomic annotation editor designed to support geographically dispersed researchers providing real-time synchronization across multiple clients, PAINT, a phylogenetically-based protein family functional annotation tool, and Noctua, an OWL-based graphical editor for richly describing the interplay of integrated gene networks and functional annotation data.

    As a full stack engineer, this individual will be responsible for designing and implementing all aspects of the technology stack, working both server-side and client-side. They will also be responsible for supporting the open-source developer community, answering questions regarding the software, and occasionally traveling for workshops and conferences both nationally and internationally. In addition they will be responsible for cross-project integration, providing functionality for the Gene Ontology Project and the Monarch Initiative, and other international collaborative software/data projects.


    • B.S. in Computer Engineering, Bioinformatics or a related field with a minimum of five years related experience, or an equivalent combination of education and experience. Advanced degree is preferred.
    • Experience in development with JavaScript in client contexts:
      • Understanding and using a variety of libraries and resources in an application
      • Client testing frameworks a plus
      • Frameworks such as Bootstrap and jQuery (UI)
      • CSS and CSS 3 (e.g. responsive layout, media queries) a plus
    • Experience in development with JavaScript in server contexts:
      • NodeJS and npm experience
      • Server unit testing frameworks
    • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat).
    • Demonstrated experience in developing robust web-based user-facing software projects.
    • Familiarity with current issues in web development and design (e.g. HTML5, WebSockets).
    • Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
    • Excellent verbal and written communication skills.
    • Ability to perform research and make independent decisions about approaches and tools to reach specific goals.
    • Ability to apply analytical skills and creativity to solve complex software and data management problems.
    • Preferred - Familiarity with genomics data and ontologies (in particular, the GO)
    • Preferred - Experience with semantically annotated data
    • Preferred - Familiarity with OWL and associated reasoners
    • Preferred - Experience with collaborative coding and build tools (github, maven, etc.)


    This is a 1-year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Laboratory in Berkeley, CA. The position may require occasional travel, weekend, and after-hours work. A background check is required.


    Rapid technological advances in genomics have transformed modern biology. From its inception, the Department of Energy Joint Genome Institute has been at the forefront of large-scale sequence-based science. Learn more at

    Lawrence Berkeley National Laboratory 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. Berkeley Lab's science is a global enterprise. Our scientists work at the frontiers of knowledge to better understand our universe and to address the challenges facing our nation and our planet. Read about our excellent benefits.


    Apply directly online at[...]11297 and follow the on-line instructions to complete the application process.


    Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status.

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