RESPONSIBILITIES:
Organization: GN-Genomics Division

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an opportunity for a skilled and creative bionformatics software developer to help us make Phytozome (http://www.phytozome.net) the most comprehensive plant genomics resource available. Phytozome combines open source bioinformatics visualization and data management tools from GMOD and related projects with advanced search and analysis components developed by JGI's Plant Genomics program, providing users with access to JGI, as well as non-JGI, plant data and analyses. Both the types and quantity of genomic and omic plant data available via Phytozome are expected to expand dramatically over the next 2 years, requiring the development of a wide range of new features, enhanced backend data systems, and increased performance. If you are an experienced JAVA/OO-Perl software developer with experience in the bioinformatics domain, come join our group and help us meet this challenge!

The selected candidate will be hired at the Software Developer 3 or 4 classification level depending upon the candidate's level of experience and qualifications.

Specific Job Duties:
Essential-

• Work as part of the team that develops and supports Phytozome (http://www.phytozome.net), a web portal and data system for plant comparative genomics.
• Extend Phytozome to allow users to query and visualize transcriptomic, gene expression, pathways, and population diversity data.
• Adapt, modify, extend and troubleshoot various open source genomic software packages (e.g, JBrowse/Gbrowse, JalView, bioperl, BioMart/InterMine, Chado) that are or will be integrated into Phytozome.
• Develop new software components in-house to provide additional functionality / superior performance as needed.
• Develop, improve, extend Phytozome's internal data interchange methods (currently XML/JAXB) and APIs to accommodate other formats (e.g, JSON) and other data systems (e.g, Kbase).
• Assist in the migration of Phytozome's backend to Chado, an open source model organism database schema.
• Develop systems for importing/processing/hosting/serving external genomic data from third party providers.

Marginal-

• Play active role in open source bioinformatics community, by contributing bug fixes and useful enhancements back to the respective projects.
• Develop video tutorials for users, make conference and training presentations, publish Bioinformatics Notes and similar methods publications.
• Monitor web statistics, determine Phytozome usage patterns.

Essential Duties for the Software Developer 4 - In addition to the required duties for a level 3, the Software Developer 4 will:

• Work at a higher level of independence and responsibilities in carrying out assignments.
• Will serve as a technical lead and key contributor called upon to troubleshoot and solve highly technical, complex problems.
• Implement a fine-grained access control system to allow coexistence of private and public data in Phytozome.
• Develop the Phytozome API and lead the migration of Phytozome's backend to Chado, an open source model organism database schema.
• Work closely with Systems Administration group to optimize hardware and configuration for maximal portal performance and stability.

REQUIREMENTS:

• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of five years of work experience, or an equivalent combination of education and experience.
• Demonstrated experience coding and debugging Java and object-oriented Perl.
• Demonstrated experience developing, deploying and maintaining web-accessible software systems on servlet or related platforms.
• Strong SQL skills, with good knowledge of database performance optimization related to schema design
• High degree of comfort on un*x command line and navigating unix file system.
• Ability to manage own development environment, modify web server and servlet configuration.
• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
• Ability to apply analytical skills and creativity to solve diverse and challenging problems.
• Detail-oriented with ability to work effectively in both team and solo environment.
• Good software development practices – self-documenting code, source control, bug tracking.

PREFERENCES:

• Advanced degree in molecular or plant biology
• Experience with the annotation plant genomes
• Experience managing genomic data

Essential Qualifications for the Software Developer 4 - In addition to the required qualifications for the Software Developer 3, the Software Developer 4 will have:

• Bachelor's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of seven years of work experience, or an equivalent combination of education and experience. Advanced degree (Masters/PhD) preferred.
• Extensive genomic analysis software experience, and substantial knowledge of various bioinformatics algorithms related to sequence analysis.
• Previous experience as a top developer on an open source genomic visualization project or genomic web portal.
• Ability to troubleshoot complex web component and database systems issues.

HOW TO APPLY:
Apply directly online at http://www.jobclub.com/banman/a.aspx?ZoneID=0&BannerID=1026&AdvertiserID=43&CampaignID=4027&Task=Click&SiteID=1&RandomNumber=915830 and follow the on-line instructions to complete the application process.

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