Software Developer/Engineer 2/3 - Phytozome

Lawrence Berkeley National Laboratory
Job Location
1 Cyclotron Rd
Berkeley, CA 94720
Job Description

Software Developer/Engineer 2/3 - Phytozome - 80943



Providing the basic “infrastructure” for life on Earth, and displaying greater genetic diversity than humans, plants possess some of the largest and most complex genomes of any living organism. The Plant Science Program at the Joint Genome Institute brings together biologists, bioinformaticians, and software engineers to sequence, analyze, organize, distribute and mine plant genomic data in support of cutting edge research worldwide in biofuels, biogeochemistry, carbon cycling and biological response to climate change.  


Phytozome web engineers play a leading role in developing the data systems and visualization platforms that allow the JGI’s scientific collaborators and plant scientists around the world to access, explore, and analyze plant genomic data. We have openings for up to 2 experienced sw engineers to work across the full web stack of the Phytozome Plant Genomics Portal (, with an eye towards radically increasing site capabilities and performance as our genomic data sets expand in size and complexity.  We expect one engineer to focus on UI development, and the other to focus more on data systems (modelling, access APIs, query optimization), but anyone joining the team should be comfortable and excited about contributing across the full web stack.


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.


The selected candidate(s) will be hired at the 2 or 3 level depending on skills and experience.


Note: below you will find an absurdly long, detailed list of job duties and qualifications.  We are a National Lab, after all!  But the tl;dr summary is:



• help our users do great science with Phytozome



• you’ve demonstrated good judgement in choosing software technologies and frameworks to deliver a web-based, big(-ish) data backed tool to your client/users

• you’ve demonstrated good design and coding skills in your implementation

• you delivered it, they loved it


Specific Responsibilities:

• Work as part of the team that develops and supports the Phytozome Portal for Plant Genomic Data

• 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

• Evaluate and help implement HDFS-based MPP data systems to supplement Phytozome’s monolithic RBDMS backend.

• Plan and implement the migration of Phytozome’s UI from a GWT-like framework to Angular2.0

• Develop advanced data visualization components and query interfaces to enable users to probe and comprehend multi-dimensional genomic data sets

• Employ solid SW Engineering practices:  design and code reviews, source control and versioning, issue tracking, unit testing, iterative development, effort estimation.


Additional desired responsibilities:

• Contribute code to best-of-breed open source genomic tools from the GMOD project ( like JBrowse and InterMine, that are integrated into Phytozome.

• Present on Phytozome alone or collaboratively at workshops, conferences, and scientific journals


In addition to the required duties for a level 2, the Software Developer/Engineer 3 will:

• Work at a higher level of independence and responsibilities in carrying out assignments.

• Work closely with Systems Administration group to optimize hardware and configuration for maximal portal performance and stability.

• Troubleshoot more complex systems and data analysis problems.


Required Qualifications:

• 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.

• Demonstrated success designing, implementing, and supporting large complex systems and software across their full life-cycle, in a scientific or technical environment.

• Excellent analytical, problem-solving and decision-making 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 Java and at least one of the following:  Python, Perl

• Experience with one or more JavaScript libs like JQuery, Dojo, SmartClient, D3.

• Demonstrated experience with JavaScript, AJAX, HTML5 and CSS

• Strong SQL skills, with good knowledge of database performance optimization related to schema design.


Additional desired qualifications:

• High degree of commandline comfort in a Un*x environment

• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.

• Experience installing/extending/configuring  genomic visualization or analysis software, especially within the GMOD universe of projects.

Experience programming multi-servlet applications

Experience building applications  with GWT, smartGWT or similar frameworks

• Solid understanding of app lifecycle in one or more of the following:  GWT, node, AngularJS

• Experience with one or more of the following non-relational databases:  HBase, MongoDB, Cassandra, Impala, Hive, SparkSQL/Shark

• Experience configuring and troubleshooting J2EE containers like Tomcat, Jetty, Glassfish


In addition to the required qualifications for the Software Developer/Engineer 2, the Software Developer/Engineer 3 will have:

• B.Sc. degree in Computer Science, Life Sciences, or related field or equivalent experience plus a minimum of 5 years of experience as a software engineer working in a team environment.  Advanced degree (MS / Ph.D.) preferred.

• Ability to troubleshoot complex web component and database systems issues.


The posting shall remain open until the position is filled, however for full consideration, please apply by September 20, 2015.


Notes:  This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career.  Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA.  Job may require occasional travel, weekend, and after-hours work.  Detailed information about the Joint Genome Institute program can be found on the World Wide Web at the following location:


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 about JGI 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. Berkeley Lab understands the postdoctoral experience in a research environment is unique. We are committed to the growth and development of early career researchers in pursuit of becoming next-generation scientists and engineers. Learn about our excellent postdoctoral benefits (


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 ( to view the poster: "Equal Employment Opportunity is the Law".

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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