[Next-Generation Sequencing Book]
  • [Photo] Bill Cannan • January 27, 2011

    BACKGROUND

    Division: Genomics Division
    Department: GN-West

    Exciting Software Developer opportunity to support The Gene Ontology Project!

    The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. At the core of the project is an ontology consisting of 30,000 classes arranged in a graph-like structure. The ontology is in the process of being integrated with other orthogonal ontologies such as the Cell Ontology, CHEBI and anatomical ontologies. The ontology is currently constructed by domain experts using OBO-Edit (Day-Richter 2007), in combination with a web-based system called TermGenie.

    With continual increases in breadth, depth and complexity, the ontology has become difficult to manage using existing tools. We are looking for an experienced and innovative software developer who can deliver a next-generation ontology editing environment, incorporating the best features of a variety of existing applications. We are also looking for a candidate who can help realize the potential of the ontology and ontology-based inferencing to better serve the curators and users of GO annotations. The candidate will also work with the developers of a number of other bio-ontologies, in particular the Cell Ontology.

    RESPONSIBILITIES

    • Gather feedback and requirements from and support the Ontology Group and GO Consortium members with the development of a next-generation ontology editing environment.
    • Devise strategies to improve the ontology construction process, and to leverage the ontology more in service of the mission of the GO.
    • Maintain OBO-Edit and improve its interoperability with other tools.
    •  Develop and integrate web-based ontology interfaces.
    •  Develop enhanced ontology visualization components.
    •  Apply analytical skills and creativity to solve diverse and challenging problems.

    REQUIREMENTS

    • B.S. in Computer Science or a related scientific or technical field (or equivalent experience) and a minimum of five years related experience
    • Demonstrated experience with Java-based software development, preferably in a bioinformatics environment
    •  Experience with both Swing and web-based application development
    •  Solid understanding of ontology languages and related description logic formalisms; Experience with text mining an advantage
    •  Good interpersonal skills and experience working with users, gathering requirements, providing user documentation, etc.

    HOW TO APPLY

    Apply directly online at http://www.jobclub.com/banman/a.aspx?ZoneID=0&BannerID=764&AdvertiserID=43&CampaignID=3126&Task=Click&SiteID=1&RandomNumber=622881 and follow the instructions to complete the application process. As part of the online application process, please submit a single attachment that includes both your resume or CV and cover letter. Please be sure to reference where you found out about the position.

    ARTICLE

    Req Number: 25423

    POLICY

    Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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