Software Developer 2/3 - Sequencing Data Management

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

Software Developer 2/3 - Sequencing Data Management - 75407
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 position available. In cooperation with other members of the Sequencing Informatics group, will be responsible for the design, implementation, testing, and deployment of extensions to, and new versions of, the JGI’s high-throughput sequence data management systems. Will also help maintain the software systems that support the production next-generation sequencing platforms. Position Reports to the Sequencing Data Management Group Lead.

The selected candidate will be hired at the Software Developer 2 or 3 classification depending upon the candidate's level of experience and qualifications.

Specific Job Duties
• Design, implement, test, and deploy extensions to the existing sequence data management systems, as well as new versions of these systems.
• Incorporate new versions of third-party software into the JGI’s sequence data management systems.
• Implement sequence data management-specific user interfaces and reports and provide additional support for new sequencing platforms and technologies as needed.
• Provide responsive customer support for new and existing sequence data management systems, including: prompt resolution of data entry errors, resolution of software malfunctions and other system needs and resolution of custom user and data retrieval requests.
• Apply analytical skills and creativity to solve problems of moderate scope.
• Follow prescribed practices for software version control, testing, and release engineering.
• Communicate regularly with customers and supervisory staff about plans, designs, and progress.
• Provide status updates in regular team meetings, and coordinate development work with other members of the Sequence Data Management team and (when appropriate) Sequencing Informatics group.

• Stay current with new sequencing technologies.
• Train biologists and other lab staff on how to use sequence data management systems.
• Analyze the impact of process, hardware or software changes on production line performance.

Essential Duties 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.
• Develop and implement substantial, known or novel, computational methods to improve the capabilities and output of the group.
• Troubleshoot more complex systems and data management problems.

Key Success Factors
• B.S. in Computer Science or a related scientific or technical field (or equivalent experience) and a minimum of two years related experience.
• Demonstrated experience with one or more of the following programming languages: Python, Perl.
• Demonstrated experience with database programming and interfaces, preferably in MySQL or Oracle.
• Demonstrated success designing and implementing systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D center or automated manufacturing facility.
• Full life-cycle software development experience with the ability to work with scientific and administrative customers to define needs and priorities
• Ability to apply analytical skills and creativity to solve moderately 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.

• Demonstrated experience with the following: JavaScript, Perl/CGI, CVS, Git.
• Demonstrated experience in providing support for production software systems.
• Experience with high performance and/or parallel computing.
• Experience developing web-based GUI.
• Experience working with scientific users.
• Experience working with bioinformatics tools and/or analysis techniques, ideally with next-generation sequencing platforms.

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 Engineering, Bioinformatics or a related field with a minimum of five years of work experience, or an equivalent combination of education and experience. MS degree is preferred.
• Demonstrated expertise creating systems and software for processing large volumes of data.
• Ability to troubleshoot complex systems and data management problems.

Contact Information: 

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

Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a safe and diverse workforce.