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RESPONSIBILITIES

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting research opportunity available for a Software Developer to support the microbial genomics and metagenomics program. Under general supervision, will develop software systems and analyze data to support microbial genome and metagenome data analysis. The work will focus on the development of front and back-end metadata systems for the Genomic Standards group. Will work independently and contributing as a member of a dynamic, multidisciplinary team of biologists, bioinformaticians, computer scientists and software developers.

The selected candidate will be hired as a Software Developer 2 or 3 depending on the candidate's level of skills and experience.

Specific Job Duties:
Essential-

Development of metadata storage and analysis systems for the Genomic Standards Group
Set up and manage the system for collection of metadata
Create AJAX-enabled metadata submission forms
Add support to local (existing and new) systems for the GSC (Genomic Standards Consortium) environmental packages
Implement public field-specific ontologies (SNOMED, Soil, Cyanobacteria, EnvoLite), modify them as necessary and incorporate them to local systems
Develop automated quality control scripts, improve data-mining and data-import pipelines
Develop data warehouse metadata statistics and add support for historical data.
Develop user interface for large scale metadata-based comparative analysis.
Apply analytical skills and creativity to troubleshoot problems of moderate scope.

Marginal-

Develop and present updates and reports at group meeting.
Participate in preparation of publications

EssentialDuties for the Software Developer 3 - In addition to the required duties for a level 2, the Software Developer 3 will:

Work at a higher level of independence and responsibilities in carrying out assignments.
Work closely with Systems Administration group to optimize hardware and configuration for maximal portal performance and stability.
Troubleshoot more complex systems and data analysis problems.

REQUIREMENTS

Key Success Factors:
Essential-

Typically requires a bachelor's degree in Biology, Computer Science, Bioinformatics or a related field with a minimum of two years experience or an equivalent combination of education and experience.
Familiarity with molecular biology, comparative genomics, metagenomics, and microbial ecology.
Demonstrated experience utilizing Java, Servlets, JPA (ideally Hibernate), web services (ideally Jersey), SQL, and UNIX.
Demonstrated strong experience utilizing disciplined and modern coding habits, such as unit testing (ideally JUnit), dependency injection (Guice or Spring DI), self-documenting code, etc.
Experience with processing and analysis of genomic and genetic data.
Strong problem-solving, decision-making, and analytical skills to make sound judgments and recommend creative solutions to diverse and challenging problems.
Strong interpersonal skills with the ability to work with scientific and administrative customers to define needs and priorities.
Ability to troubleshoot diverse systems and data analysis problems.

Marginal-

Exposure to parallel programming and MPI
Interest and facility in algorithmic research involving graph theory, string comparison, or other bioinformatically-relevant areas of computer science

Essential Qualifications for the Software Developer 3 - In addition to the required qualifications for the Software Developer 2, the Software Developer 3 will have:

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. Advanced degree (MS / Ph.D.) preferred.
Extensive genomic analysis software experience, and substantial knowledge of various bioinformatics algorithms related to sequence analysis.
Must demonstrate detailed knowledge and strong technical ability in full life-cycle software development, database design and access, web user interface design, development and deployment
Ability to troubleshoot complex web component and database systems issues.

TERMS

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. The position may require occasional travel, and weekend/after-hours work. Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA. A background check is required. (The job posting was revised slightly on Sept., 22, 2014.)

ABOUT US

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 http://www.jgi.doe.gov

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 (http://ucnet.universityofcalifornia.edu/compensation-and-benefits/health-plans/index.html).

HOW TO APPLY

Apply directly online at http://50.73.55.13/counter.php?id=258216 and follow the instructions to complete the application process.

POLICY

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. http://www.lbl.gov

Discussion forums: Opportunity: Software Developer 2/3 -- Microbial Genomics and Metagenomics Program (#80407) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)

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