News/Software Developer - Phytozome

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Software Developer 3/4 - Phytozome - 74226
Organization: GN-Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for an experienced Software Developer / Engineer to support the Phytozome group. The Phytozome group in the JGI Plant Genomics Program is responsible for the annotation and analysis of plant genomes, and for providing both internal and external users with visualization, querying and data access capabilities to facilitate progress in fundamental, biofuel and climate-related Plant science. The Phytozome website and associated databases and analysis tools provide JGI’s collaborators and the broader plant biology community with intuitive and powerful interfaces to access and explore plant genomic data. As the JGI anticipates a massive increase in RNA-Seq and resequencing output, we have an opportunity for an experienced developer to help us enhance and expand Phytozome to host even more plant genomes and their annotations, and to develop new databases and interfaces to support users’ exploration of plant genomic diversity and gene expression data.

Under broad supervision, the ideal candidate will develop, implement, test, integrate and deploy new and/or existing software components of the Phytozome system for the visualization and querying of plant genomic and related data. They should demonstrate detailed knowledge and strong technical ability in web user interface design concepts and implementation, data modeling, and database schema design, as well as extensive familiarity with standard genomic sequence data types and analysis methods.

The selected candidate will be hired at the Software Developer 3 or 4 classification level depending upon the candidate's level of experience and qualifications. Position reports to the Phytozome Group Lead.

Specific Job Duties


  • Work as a member of the Phytozome development team to create, maintain and extend the suite of visualization, backend, and data management tools that support the public interface to the JGI’s Plant Genomics program.
  • Create and maintain database-backed web applications for the display and querying of genomic data.
  • Evaluate the suitability of third party open source tools (e.g. GMOD) versus in-house development to provide desired functionality to Phytozome.
  • Optimize the Phytozome user experience by constantly monitoring and improving backend data retrieval performance (as determined by benchmarking) and front-end usability (as determined by user surveys and best practices).
  • Follow best practices for software version control, documentation, testing and release engineering.


  • Work with Phytozome/Metazome internal and external user community and Scientific Advisory Board to prioritize new feature requests, and provide accurate estimates of implementation timelines.
  • Assist in the preparation of manuscripts, tutorials and conference presentations based on Phytozome.
  • Work with JGI’s Systems group to anticipate hardware needs for increasing data set sizes and expanded functionality.

Essential duties for the Software Developer 4 - In addition to the job duties described above, the Software Developer 4 will:

  • Operate at a higher level of independence and responsibility when carrying out assignments.
  • Will serve as a technical lead and key contributor called upon to solve highly technical, complex problems.

Key Success Factors

Essential -

  • B.S. in technical or scientific field (or equivalent experience) and a minimum of five years programming experience.
  • Minimum five years experience and demonstrated success designing and implementing bioinformatics analysis systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D.
  • Familiarity with standard genomic sequence data repositories (e.g, GenBank, SwissProt) and functional classification databases and ontologies (e.g., KEGG, Panther, Metacyc, GO).
  • Solid experience programming with object-oriented Perl and Java.
  • Advanced knowledge of SQL and relational database design.
  • High degree of comfort developing on, and for, linux systems.
  • Demonstrated experience developing database-backed applications and experience with web technologies including: Apache, Tomcat, CGI programming, JDBC, JAXB, GWT, AJAX.
  • Ability to effectively learn and apply new technical concepts to troubleshoot and solve problems and challenges of a diverse scope.
  • Effective interpersonal communication and presentation skills.
  • Effective time management, organization, and planning skills.
  • Ability to work effectively in a diverse team environment.

Desirable -

  • M.S./Ph.D. in Molecular Biology, Genetics or related field.
  • Mathematical sophistication to understand algorithmic concepts behind sequence alignment, gene family clustering, and phylogenetic tree building.
  • Experience with the management and visualization of gene expression and genomic diversity data.
  • Solid understanding of statistics.
  • Experience developing software that includes or interacts with GMOD and bioperl components.
  • Working knowledge of Python and PHP.

Essential Qualifications for the Software Developer 4 - In addition to the qualifications listed above, the Software Developer 4 requires:

  • A minimum of eight years related experience.
  • Demonstrated ability to solve highly complex problems and work independently on end-to-end implementation and maintenance of software projects through multiple releases.

How To Apply: Apply directly online and follow the instructions to complete the application process.

Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

Posted to the GMOD News on 2012/05/16