BACKGROUND

The Berkeley Bioinformatics and Ontologies Project (BBOP), located at Lawrence Berkeley National Laboratory, has a unique opportunity for a computer scientist to take over the development and maintenance of OBO-Edit, which is funded by the Gene Ontology Consortium. The BBOP is a founding member of the Gene Ontology Consortium, and a part of the National Center for Biomedical Ontology. We have a long history of developing open source software and databases for Drosophila and other organisms, and are an original member of the Generic Model Organism Database project. We are an extremely collaborative team, creatively sharing ideas among bright individuals. Learn more at http://www.berkeleybop.org.

RESPONSIBILITIES

The OBO-Edit Developer position is responsible for the maintenance and future development of OBO-Edit as well as for the long range vision and to some extent, for the OBO ontology effort and the Gene Ontology as a whole. OBO-Edit is a Java application for editing biological ontologies, It has underlying Java libraries which are used in a growing number of bioinformatics applications. The developer is responsible for maintaining and expanding these libraries for use by external software development projects. These responsibilities include code documentation and creating technical overviews on the OBO-Edit Developer’s wiki.

In addition to software development responsibilities, the OBO-Edit Developer assumes a key role in the growing OBO-Edit user community. This includes organizing twice-monthly online meetings of the working group, providing progress reports and receiving feedback on regular software demonstrations. In addition, the developer has weekly online "office hours" for users to ask questions and provide feedback. The developer maintains the oboedit.org Web site and the wiki, and constantly monitors the working group mailing list.

OBO-Edit and its associated software libraries are the reference implementation for the OBO file format specification. The developer of OBO-Edit is responsible for keeping OBO-Edit synchronized with the ontology syntax and semantics specified by the latest OBO specification. The developer regularly participates in and presents at scientific conferences that are relevant to OBO-Edit and biological ontologies in general. Collaboration with the BBOP and the OBO-Edit working group on relevant scientific publications and posters are also part of this work.

REQUIREMENTS

• Significant experience developing large Java graphical user interface applications
• Knowledge of biology, and familiarity with ontologies or related fields such as logic, philosophy or linguistics
• Excellent Java programming skills and significant experience developing large Java Swing applications
• Expertise in a wide array of computer science disciplines (E.g., user interface design, graph algorithms, reasoner design, parser design, relational databases, and compiler design)
• Familiarity with agile programming techniques, particularly software unit testing
• Excellent interpersonal and communication skills necessary to interact with users from around the world, using instant messaging, e-mail and video conferencing

LOCALE: Berkeley, CA - U.S.A.

HOW TO APPLY

http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21106&p=1.

Submit a single attachment including your résumé and cover letter. Reference “Internet� and “Bioinformatics.org� as your source. LBNL is an AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov.