Software Developer 3

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

Software Developer 3 (Integrated Fungal Genomics) - 79510
Organization: GN-Genomics

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 develop MycoCosm (, the integrated fungal genomics resource. MycoCosm combines visualization and analysis tools, provides users with access to JGI and non-JGI fungal genomics data. With expected dramatic expansion of genomics data due to significantly increase genome sequencing, MycoCosm requires development of a wide range of new front end and backend features for easy use and high performance. We are looking for JAVA/JavaScript software developer with technical expertise in developing web applications and relational databases, experienced in the bioinformatics domain.

Key Responsibilities:
• Work as part of the team that develops and supports MycoCosm (, a web portal and data system for fungal comparative genomics.
• Design and develop software for the MycoCosm/Fungal Program.
• Design effective solutions compatible with existing systems.
• Interface with end-users to gather feedback and requirements.
• Provide daily client support, including occasional evening and weekends.
• Participate in system architectural review and design.
• Observe and promote configuration management and deployment policies.
• Participate in formal and informal design and code reviews.
• Apply analytical skills and creativity to troubleshoot problems of diverse scope.
• Monitor web statistics, determine MycoCosm usage patterns.
• Create documentation and training materials


• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of five years of work experience, or overall equivalent experience
• Demonstrated success designing, implementing, and supporting large complex systems and software in a scientific or technical environment
• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems
• Experience with genomics data, analytical tools and methods
• Demonstrated experience coding and debugging Java and object-oriented Perl
• Expertise with web development: HTML, CSS and Javascript
• Strong SQL skills, with good knowledge of database performance optimization related to schema design
• Excellent analytical, problem-solving and decision-making skills to independently make sound judgments and creative solutions to complex problems.
• Effective time management, organization and planning skills; ability to work effectively in team environment
• Ability to apply analytical skills and creativity to solve diverse and challenging problems
• Good software development practices – self-documenting code, source control, bug tracking

• Experience with SGE or other HPC environments.
• Experience with large MySQL-based data sets.

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.

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

How To Apply
Apply directly online at and follow the on-line instructions to complete the application process.

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