Web Developer 2 (Phytozome Plant Genomics Portal) - 81593

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

Web Developer 2 (Phytozome Plant Genomics Portal) - 81593
Organization:  JG-Joint Genome Institute

Berkeley Lab is Bringing Science Solutions to the World, and YOU can be a part of it!

In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with "excellence." That's why we hire the best - whether in research, finance or other operations. This is a great opportunity to bring your top-notch skills to bear in support of world-class scientific research that addresses national and global challenges!

Position Summary:
Berkeley Lab’s Joint Genome Institute (JGI) has an immediate opening for a Web Developer for the Phytozome Plant Genomics Portal. Our team of bioinformaticians, biologists and software engineers turn multi terabytes of raw genome sequences into biologically informative reference datasets and analyses, in support of cutting edge, publicly accessible research worldwide in biofuels, plant evolution and plant adaptation to climate change. As Phytozome’s main UI developer, you will make major contributions to the ongoing design and development of a robust, elegant and scalable analysis and visualization platform that enables JGI’s scientific collaborators and plant scientists around the world to access, explore, and analyze plant genomic data.

The Phytozome team collaborates with several local as well as international teams in the areas of plant genome structural and functional annotation, genomic data modelling, and web based genomic tool development. Our team members have many opportunities to contribute to these collaborations.

What You Will Do:
• Work as part of the team that develops and supports the Phytozome Portal
• Continuously debug, improve and extend the Phytozome Portal to accommodate more diverse and ever larger genomic data sets, ensuring our users can produce the best science possible with our tools
• Plan and implement the migration of Phytozome’s UI from GWT to a modern javascript framework
• Develop advanced data visualization components to enable users to probe and comprehend multi­dimensional genomic data sets
• Employ solid SW Engineering practices: design and code reviews, source control and versioning, issue tracking, unit testing, iterative development, effort estimation
• Present on Phytozome alone or collaboratively at workshops, conferences, and scientific journals


What Is Required:
• B.S. Degree in Computer Science, Bioinformatics, Life Sciences, or related field with minimum two years of programming experience. Or an equivalent combination of education and experience.
• Experience in at least one MV* javascript framework, such as Express+Angular+Node, React+Fluxxor, Ember.
• Demonstrated success designing, implementing, and supporting moderately complex systems and software across their full life­cycle
• Excellent analytical, problem solving and decision­making skills to independently make sound judgments and creative solutions to moderately complex problems.
• Effective time management, organization and planning skills; ability to work effectively in team environment.
• Demonstrated experience with JavaScript, AJAX, HTML5 and CSS

Additional Desired Qualifications:
• Moderate level of command line comfort in a Un*x environment
• Experience with visualization tools for data intensive science (R, d3, canvasXpress, CanvasJS, BioJS)
• Comfort with relational database concepts and SQL
• Experience with jQuery, bootstrap, and one or more of java/python/perl.
• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
• Experience building applications with GWT, smartGWT or similar frameworks
• Experience with one or more of the following databases: mySQL, postgreSQL, MongoDB
• Experience with Lucene/Solr/ElasticSearch or similar search systems
• Experience configuring and troubleshooting J2EE containers such as Tomcat

Notes: This is a 1-year, term appointment with the possibility of renewal and with the possibility of conversion to career.

This position requires completion of a background check.

Berkeley Lab 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. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Click here (http://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf) to view the poster: "Equal Employment Opportunity is the Law".

How to Apply

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

A part of the proposed tax bill in the US could make tuition waivers taxable, Vox reports.

The New York Times reports that only a subset of STEM worker are in demand.

US News & World Report says students pursuing STEM degrees should consider what they are getting into.

New study finds bias against female lecturers among student course evaluations, the Economist reports.