Software Developer 4 - Genomics OnLine Database

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

Software Developer 4 - Genomics OnLine Database - 80526
Organization:  GN-Genomics

Under broad supervision, will gather feedback and requirements to develop systems that support the growing curation of metadata from multiple scientific programs across JGI and outside systems. Will work closely with the microbial and metagenomics programs and will lead the development of the Genomics OnLine Database (GOLD), including the integration of project and metadata information.  Will implement QC rules and develop other tools to enable the sharing and exchange of metadata from JGI projects and develop interfaces for the JGI’s Integrated Tracking System (ITS).  Will collaborate with various internal groups to support the full GSG compliance of any data and metadata submitted to bioproject, biosample, GenBank and SRA. In addition, will work on highly technical, complex problems including analysis, evaluation and implementation of controlled vocabularies for the description of metadata in coordination with the JGI’s integrating tracking system, the Genomics Standards Consortium and other ontologies. This position will be under the general supervision of, and will report to, the Prokaryotic super program head.

Specific Job Duties
• Lead the development of the Genomics OnLine Database (GOLD)including maintaining and developing the GOLD back and front end to facilitate the storage, display and editing of metadata of JGI projects.
• Gather feedback and requirements to develop and implement QC rules and apply patterns for automatic filling of metadata to minimize manual effort.
• Build scripts to parse and quality control(QC) final deliverable import Excel files.
• Overlook, share, exchange, import and sync the final deliverable excels to and from ITS.
• Build and develop web services to enable the continuing share and exchange of metadata between ITS, Genome Portal, NCBI, annotation pipelines and analysis systems.
• Create and be in charge of service tickets pertaining to metadata corrections in the ITS system.
• Extend and advocate the support of the full GSG compliance of any data and metadata submitted to bioproject, biosample, GenBank and SRA.
• Collaborate with various internal groups including Genome Portal, Project Management, Rolling QC and annotation/analysis groups to ensure smooth processing and flow of metadata from beginning to the end of a JGI project's lifecycle.
• Will serve as a technical lead and key contributor called upon to troubleshoot and solve highly technical, complex problems.
• Develop the Phytozome API and lead the migration of Phytozome’s back-end 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.

• Attend standing project planning and review meetings as well as standing meetings with the other JGI Groups.
• Participate in presentations and discussions about the team's work.
• Participate in software release testing.


Key Success Factors
• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of eight years of work experience, or an equivalent combination of education and experience.
• In-depth programming experience coding and debugging Java.
• Demonstrated experience developing, deploying, maintaining web-accessible software systems on servlet or related platforms.
• Strong SQL skills with good knowledge of Oracle database performance optimization related to schema design.
• Demonstrated experience using and optimizing Hibernate and Tomcat connection pooling, for optimal performance on an Oracle database.
• High degree of comfort on UN*X command line and navigating UN*X file system.
• Ability to manage own development environment, modify web server and servlet configuration.
• Excellent working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
• Detail-oriented with ability to work effectively in both team and solo environment.
• Excellent knowledge and experience with software development practices – dependency injection, interfaces, self-documenting code, source control, bug tracking.
• Exceptional oral and written communication skills, including public-speaking and presentation skills.
• Ability to apply analytical skills and creativity to solve highly technical/complex problems.
• Effective time management, organization, and planning skills with the ability to allocate resources and assign work to meet goals and deadlines.
• Talent for working well under short deadlines and handling multiple tasks simultaneously.
• Excellent customer service skills.

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.

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