Software Developer (Genome Portal and Sequence Data Management) | GenomeWeb

Software Developer (Genome Portal and Sequence Data Management)

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

Software Developer (Genome Portal and Sequence Data Management) - 78957
Organization: GN-Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting software developer/programmer opportunity available in the Sequence Data Management and Genome Portal groups. The group is small in number but has a breadth that includes data management, programming, architecture, and software design. The best-fit individual will be savvy with programming and data curation, and will articulate across disciplines and position levels to get important work done.

This role provides the opportunity to:
• Produce and manage the sequence data from next-generation sequencers that support global genomic and bio-energy research science
• Work with large scale data problems
• Work with petabyte range file and tape systems
• Be part of the team that works with the world’s fastest computers for computationally intensive projects

The work is equal parts programming and data management. This includes supporting the implementation of data exchange between JGI and KBase ( Will also work with petabytes of data and metadata to facilitate data finding/sharing.

Responsibilities (Software Developer 3 level):
• Develop and maintain KBase facing Genome Portal UI code; develop customer facing web pages.
• Help maintain software systems that support data transfer between JGI and KBase.
• Design, implement, test, and deploy extensions to high-throughput data management systems.
• Analyze the impact of process, hardware and software changes on production line performance.
• Implement sequence data management, specific user interfaces and reports.
• Ensure accurate software version control, testing, and release engineering.
• Communicate plans, designs, and progress/status to customers and management; coordinate development work across JGI groups.
• Work with internal groups to facilitate JGI’s metadata standards
• Assist with the curation of legacy data files and metadata
• Troubleshoot and resolve issues with new and existing sequence data management systems (e.g., processing errors, software bugs, user and data retrieval requests).

In addition to the above, the following are Software Developer 4 responsibilities:
• Contribute at a higher level of independence and responsibilities.
• Perform as a technical lead and key contributor; troubleshoot and solve highly technical, complex problems.


Qualifications (Software Developer 3 level):
• B.S. in Computer Science or a related scientific/technical field plus typically five years of related experience, or overall equivalent
• Proficiency with Java, JavaScript and Python; MySQL or Oracle (or similar); Linux or Unix
• Experience developing web user interfaces
• Full life-cycle software development experience with the ability to communicate effectively (i.e., understand/define needs and priorities) with scientific and administrative customers
• Ability to apply analytical skills and creativity to solve complex software and data management problems
• Effective time management, organization, and planning skills
• Talent for working well under short deadlines and handling multiple tasks simultaneously
• Ability to work effectively in a diverse team environment
• Python, JavaScript, Git/Bitbucket
• Production software systems support experience
• High performance, parallel computing, and/or grid engines
• Agile and Test-Driven development methodologies
• Design and utilization of interface services (e.g., RESTful)
• Demonstrated expertise creating systems and software for processing large volumes of data

In addition to the above, the following are Software Developer 4 qualifications:
• Bachelor's degree in Computer Science, Bioinformatics or related field plus a minimum of seven years of relevant experience, or overall equivalent; advanced degree (Masters/PhD) preferred.
• Proficiency with system and software design/implementation in a scientific or technical environment
• Experience troubleshooting complex software issues

Notes: A single 1-year term appointment (employee status; not contractor) will be hired at the classification level appropriate with the successful candidate’s relevant breadth and depth of experience. The appointment may renew and/or convert to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA. (The posting was updated on October 7, 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 aboutJGI happenings at and

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

How to Apply

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

About Our Organization

The GRE isn't a good predictor of graduate school performance or productivity, according to two PLOS One studies.

Bitesize Bio has some advice for scientists ready to leave their current lab behind.

A trio of editors from the Nature family of journals describes what make a peer review a good one.

Spots in genetic counseling training programs are competitive, Maclean's reports.