[Gmod-help] GMOD Job Posting

[Jennifer Reddell]

The below job opportunity was emailed on 4/18 to be posted on the  
GMOD but I'm not able to find it.  Can someone help me?  I can't  
figure out how to post it.


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
Essential
• 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.

Marginal
• 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 at http://bit.ly/LBL74226GMOD 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.




Jennifer Reddell
Ad Club Advertising
Direct: 209.343.1914
Toll Free: 800.333.1228
Toll Free Fax: 800.759.4675
jennifer at adclub.com


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