DESCRIPTION

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 (http://phytozome.jgi.doe.gov), 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:

Responsibilities:

Help our users do great science with Phytozome

Qualifications:

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 (http://gmod.org) 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.

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