Lawrence Berkeley National Laboratory

Walnut Creek, CA | Posted: 5 years ago

Data Scientist - 86474 Organization: JG-Joint Genome Institute

The U.S Department of Energy (DOE) Joint Genome Institute (JGI) has an opening for a Data Scientist in the Integrated Microbial Genomes (IMG) Group.

The IMG Group develops and maintains IMG (https://img.jgi.doe.gov/), a data system that serves as a resource for the scientific community to enable the analysis and annotation of genome and metagenome data in a comprehensive comparative context. It is one of the most widely used systems for this purpose, serving a community of more than 20,000 users all over the world. The IMG team works closely with users of the JGI, as well as JGI-internal Science Programs including the Metagenome Program (https://jgi.doe.gov/our-science/science-programs/metagenomics/), the Microbial Genomics Program (https://jgi.doe.gov/our-science/science-programs/microbial-genomics/), and the Microbiome Data Science (https://jgi.doe.gov/our-science/scientists-jgi/microbiome-data-science/) group.

This position will be in the IMG Pipeline Group, will report to the IMG Group Pipeline team lead, and will be responsible for the management and development of sequence data pipelines. Depending on qualifications, this position may be at the Data Scientist 2 or 3 level.

Data Scientist (Level 2) Specific Responsibilities:

• Manage the submission of JGI genomes in IMG to NCBI GenBank
• Develop and deploy in production new types of Omics analysis pipelines
• Maintain and improve the existing miscroservice for Average Nucleotide Identity calculations
• Resolve issues reported by users and provide support to internal and external IMG users
• Develop and present updates and reports at meetings.
• Support internal and external users with data exchange and custom data analysis.

In addition to the above, Data Scientist (Level 3) Specific Responsibilities:

• Investigate and provide additional microservices
• Troubleshoot GenBank submission problems. Interact with peers with expertise extending beyond the area of specialization within the Science Programs and DSI department to ensure efficient communication and completion of analysis projects.
• Make presentations at the Microbial Genomes & Microbiomes (MGM) Workshop regularly held at JGI.
• Provide guidance to junior members in the IMG Group.

Data Scientist (Level 2) Required Qualifications:

• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of 5 years of work experience, or an equivalent combination of education and experience.
• Demonstrated expertise and experience processing large volumes of data, whole-genome data analysis, and comparative genomics.

Data Scientist (Level 2) Preferred Qualifications:

• Advanced degree (MS / Ph.D.).
• Demonstrated experience working in similar fields.
• Demonstrated experience working in high-performance computing.
• Demonstrated experience working in microservices.
• Experience and skill in preparing research publications.

In addition to the above, Data Scientist (Level 3) Required Qualifications:

• Minimum of 8 years of related experience with a Bachelor’s degree; or 6 years and a Master’s degree; or equivalent experience.
• Excellent track record of success in previous employment.

Additional Qualifications for the Data Scientist (Level 2 & 3):

• Prior experience and demonstrated an ability to troubleshoot complex systems and data analysis problems.
• Prior experience and demonstrated an ability to contribute to the development of multiple projects/pipelines.
• Proven ability to program in one or more of the following programming languages: Python, Perl, Java, GO, and C/C++.
• Familiar with SQL databases such as Oracle, MySQL or Postgres.
• Familiar with advanced UNIX utilities and shell programming.
• Familiar with existing Bioinformatics databases, tools, and best practices
• Understanding of standard sequencing analysis methods (assembly, gene calling, functional annotation).
• Strong problem-solving, decision-making, and analytical skills to make sound judgments and recommend creative solutions to moderately complex problems.
• Excellent writing, interpersonal communication, and presentation skills.
• Demonstrated ability to work independently and collaboratively and as a team member in a diverse team environment.
• Having a wide-ranging of knowledge and experience in different genomic analysis methods.

The posting shall remain open until the position is filled.

Notes:

• This is a full time, 2-year term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
• Classification will depend upon the applicant's level of skills, knowledge, and abilities. (For dual postings - add this to the position summary at the end of the paragraph) This position will be filled at the Data Scientist 2 or Data Scientist 3 level, dependent on experience.
• Full-time, M-F, exempt (monthly paid) from overtime pay.
• Salary is commensurate with experience.
• This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
• Work will be primarily performed at DOE Joint Genome Institute (JGI) — 2800 Mitchell Dr., Walnut Creek, CA.

How To Apply Apply directly online at http://50.73.55.13/counter.php?id=157669 and follow the on-line instructions to complete the application process.

About the JGI: The JGI is a DOE Office of Science national user facility of Lawrence Berkeley National Laboratory (Berkeley Lab), focused on integrative and collaborative genome science and managed by the University of California. The JGI enables its users to harness its resources and integrated capabilities, at no cost, in high-throughput sequencing, DNA design and synthesis, metabolomics and computational analysis in support of DOE missions related to bioenergy and environmental applications.

About Berkeley Lab: Berkeley Lab (LBNL, http://www.lbl.gov/) 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. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

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