RESPONSIBILITIES:
Division: Genomics Division
Department: Computational Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting opportunity available for an experienced Bioinformatics Analyst. Under general supervision will work in a small team as a Population Genetics Analyst to design resequencing experiments to enable the study of plant population dynamics, diversity and substructure. Will perform analysis of data related to plant genomic projects, with strong emphasis on characterizing genomic diversity. Will be responsible for obtaining plant genome data from internal or external sources and configuring and running software for processing and analysis including; sequence alignment, SNP detection and development of tools and methods for interpreting variation data among dozens of plant cultivars, phylogenetic tree construction, linkage analysis, and statistical analysis. Will also store and organize results for presentation and viewing by the JGI's collaborators and the wider scientific community and help devise and perform tests to asses the quality of input and output data. Position reports to the manager of the Plant Genome Diversity group.

Specific Job Duties:
Data Processing:

• Collect and organize plant genome data (internal or public databases, collaborators, etc.)
• Configure, run, and troubleshoot a wide variety of data analysis software, including sequence alignment tools (e.g. BWA, Gmap, BLAST, clustalW), phylogenetic tree building packages (e.g. PHYLIP), statistical analysis software (e.g. R), as well as proprietary software. Resource-intensive analysis is performed in a Sun Grid Engine environment.
• Assess quality of input data and results.
• Maintain a work log on performed analysis and configurations. Provide feedback to improve protocols, methods and tools for plant genome analysis.

Tool and Protocol Development:

• In collaboration with scientific programmers and software developers in the group, work on validation and optimization of methods of data analysis.
• Help maintain a "best practices" protocol outlining details of specific analysis methods and software.

User Support:

• Communicate with internal and external users regarding current projects including timelines and updates.
• Develop and present updates and reports on results to the group.
• Support internal and external collaborators with data exchange and custom data analysis

Essential Duties for the Bioinformatics Analyst 3 - In addition to the required duties for a level 2 Analyst, the level 3 Analyst will:

• Work at a higher level of independence and responsibilities in carrying out assignments.
• Develop and implement substantial, known or novel, computational methods to improve the analysis capabilities and output of the group.
• Troubleshoot more complex systems and data analysis problems.

REQUIREMENTS:
Key Success Factors:

• Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of two years of work experience, or an equivalent combination of education and experience (Advanced Degree preferred but not required)
• Proven detailed understanding of population genetic modeling including previously published scientific papers within this field
• Knowledge of standard bioinformatics methods and tools for gene and protein sequence analysis
• Experience with installing and executing software and scripts in a UNIX/LINUX environment
• Working knowledge of PERL and SQL
• Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to complex problems
• Detail-oriented with strong organizational skills to address user needs in an effective and timely manner

Essential Qualifications for the Systems Analyst 3 - In addition to the required qualifications for the Systems Analyst 2, the Systems Analyst 3 will have:

• MS or Ph.D. degree in Biology, Bioinformatics, Computer Science or related field preferred with a minimum of five years of work experience, or an equivalent combination of education and experience
• Solid experience in processing large volumes of data, whole-genome data analysis, phylogenetics, and comparative genomics
• Ability to troubleshoot complex systems and data analysis problems

TERMS:
This is a one year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. 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: http://www.jgi.doe.gov.

HOW TO APPLY:
To apply please click the link below to be redirected to the lab job posting, then following the online instructions to complete the application process

http://www.jobclub.com/banman/a.aspx?ZoneID=0&BannerID=579&AdvertiserID=43&CampaignID=2256&Task=Click&SiteID=1&RandomNumber=380188

ARTICLE: Req. Number: 23852

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