Java Software Engineer - Microbial Genomics and Metagenomics Program

Lawrence Berkeley National Laboratory
Job Location
Walnut Creek, CA 94598
Job Description

Java Software Engineer - Microbial Genomics and Metagenomics Program - 80407
Organization:  GN-Genomics

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 Java 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 both independently and as part of a dynamic, multidisciplinary team of software developers, biologists, bioinformaticians, and computer scientists.

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

Specific Job Duties
• Development of metadata storage and analysis systems for the Genomic Standards Group
• Set up and manage Java-related systems, web services, and scripts (both stand-alone and web-based) for collecting, storing, and editing metadata, from internal and public sources.
• Develop automated quality control scripts, improve data-mining and data-import pipelines.
• Develop user interface for large scale metadata-based comparative analysis.
• Add support to local (existing and new) systems for GSC (Genomic Standards
• Consortium) environmental packages.
• Develop data warehouse metadata statistics and add support for historical data.
• Apply analytical skills and creativity to troubleshoot problems of a moderate scope.

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

Essential Duties for the Software Developer/Engineer 3 - In addition to the required duties for a level 2, the Software Developer/Engineer 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.


Key Success Factors
• Typically requires a bachelor’s degree in Computer Science, or a related field with a minimum of two years professional java development experience or an equivalent combination of education and experience.
• Demonstrated experience using Java, Servlets, JPA (ideally Hibernate), web services (ideally Jersey), SQL, JPQL, and UNIX.
• Demonstrated experience utilizing disciplined and modern coding habits, such as unit testing (ideally JUnit), dependency injection (Guice or Spring DI), self-documenting code, etc.
• Familiarity with (or interest in) molecular biology, comparative genomics, metagenomics, and microbial ecology.
• Strong problem-solving, decision-making, and analytical skills, to make sound judgments and recommend creative solutions to moderately complex problems.
• Strong interpersonal skills, to work with scientific and administrative customers to define needs and priorities.
• Ability to troubleshoot complex systems and data analysis problems.

• Prior experience processing and analyzing genomic and genetic data.
• Exposure to (or interest in) 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/Engineer 3 - In addition to the required qualifications for the Software Developer/Engineer 2, the Software Developer/Engineer 3 will have:
• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of five years of professional Java development experience, or an equivalent combination of education and experience.  Advanced degree (MS / Ph.D.) preferred.
• 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.

Notes: 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

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 (  

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.

How to Apply

Apply directly online at and follow the instructions to complete the application process.

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