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    Opportunity: Bioinformaticist / Software Developer 2 (Berkeley Bioinformatics Open-Source Projects) (#79554) @ 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 a Bioinformaticist (Software Developer 2). This position opens the door to growth opportunities in computational genomics. The current explosion of molecular data means there is also a demand for people who can build the bridges between the latest technology developments that will meet the challenges of medical diagnosis, systems biology, and biodiversity.

    The successful candidate will work in a positive environment that recognizes and values the contribution of every team member. People who are enthusiastic and energized by the idea of contributing to fundamental research insights into genes, pathways, gene expression, protein and genetic interactions, orthology, disease, and phenotypes.

    The Berkeley Bioinformatics Open-Source Projects (BBOP) is dedicated to developing tools and applying computational technologies that address biological research questions. Since 2003, BBOP has been supported by NIH research grants to develop and apply 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).


    BBOP is seeking an bioinformaticist who will contribute to all aspects of software development cycles and infrastructure, including initial R&D, developing test suites, deployment to production systems, and maintenance once software is released to the biological research community.

    Initially the primary role will be supporting the GOC, in particular the AmiGO web-based tools for searching and browsing the terms and gene product annotations described by the Gene Ontology. AmiGO's component parts are currently broken into three modules: the GOlr backend (a Solr document store), some legacy Perl in the frontend, and a JavaScript UI and API that communicates directly with the GOlr backend.


    This position requires the ability to: deliver bug fixes, changes, and features quickly; test and evaluate alternative technologies (e.g. Rhino vs. V8); develop effective test suites; handle user issues; and provide system reliability with minimal downtime.
    • B.S. in Computer Science, Bioinformatics or a related field with a minimum of two years related experience, or an equivalent combination of education and experience; M.S. degree is preferred.
    • Experience with collaborative coding and build tools (Jira, Confluence, SVN, Git, maven)
    • Proficient experience with Debian-based GNU/Linux systems (Ubuntu a plus)
    • Experience with "Cloud" and virtual machine management using KVM (libvirt tools a plus)
    • Experience with development for and deployment to cloud/PaaS: AWS, Heroku, OpenShift, etc.
    • Client and server unit test experience (Selenium, HTMLUnit, etc.)
    • Experience with system monitoring (e.g. Nagios, Munin)
    • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat)
    • Demonstrable fluency in Perl (server-side)
    • Experience with installing and tuning of common software servers and services (e.g. LAMP, Jetty + Solr, Apache, Nginx, Tomcat, Jenkins, OpenSSH, MySQL, Postgre, etc.)
    • Experience with Drupal deployment, development, and management: PHP, Drupal plugin, and theme development a plus. Transferable skill sets with similar CMSs a plus.
    • Preferred - Familiarity with JavaScript (client-side)
    • Preferred - Experience with big data wrangling, particularly genomic data
    • Preferred - Experience with team approaches to software construction
    • Preferred - Experience with RAID and LVM
    • Preferred - Experience with bulk administration and setup tools: apt-dater, Puppet, etc; Debian packaging
    • Preferred - Familiarity with networking and file systems (NFS and Fibre Channel)
    • Preferred - Experience with system/data backup and system/data recovery methods


    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[...]11303 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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