Bioinformatics Associate Data Scientist

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Information Technology
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JG-Joint Genome Institute
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86097 Requisition #

The Department of Energy Joint Genome Institute (DOE JGI, a division of Berkeley Lab) is looking for a Bioinformatics Data Scientist with a strong background in data mining and software development, with a particular emphasis on the data and methods related to functional annotation and metabolic reconstruction. Of specific interest is familiarity with major annotation and pathway databases and ontologies, knowledge of major bioinformatics tools for pairwise and multiple sequence alignment, profile alignment, phylogenetic tree reconstruction, and prior experience with benchmarking of bioinformatics tools and software. The incumbent is expected to work both independently, and as part of a team of biologists, bioinformaticists and software engineers to develop software and data framework for accurate functional annotation of microbial genomes and metagenomes, reconstruction of reaction networks and microbial phenotype inference. This position will be filled at the Data Scientist (Level 1) or Data Scientist (Level 2), dependent on experience.

Data Scientist (Level 1) Specific Responsibilities:

  • Work on designing and implementing a framework for accurate functional annotation and pathway reconstruction by collating the data and metadata from various data sources, and supporting manual curation efforts.

  • Work with the Integrated Microbial Genomes & Microbiomes (IMG) data warehouse team to ensure accurate representation of functional annotation and pathway data in IMG and support for major annotation and pathway analysis needs by IMG users.

  • Work with the DOE Systems Biology Knowledgebase (Kbase) team to ensure data portability and support for functional annotation and pathway analysis needs by Kbase users.

  • Contribute to the development of IMG pipelines through the selection of appropriate software, benchmarking and testing of existing and newly developed software, and providing feedback to troubleshoot and recommend solutions.

  • Create documentation and training materials.

In addition to the above, Data Scientist (Level 2) Specific Responsibilities:

  • Independently identify resources of functional annotation and pathway data and develop the software to mine them in an automated manner

  • Work with the Integrated Microbial Genomes & Microbiomes (IMG) data warehouse team to implement a scalable and portable pipeline to update functional annotations and pathway reconstructions for thousands of genomes and metagenomes

  • Facilitate the training and transfer of knowledge of technologies to other group members in the division.

  • Develop qualitative and predictive analytics to inform organizational policy.

Data Scientist (Level 1) Required Qualifications:

  • B.Sc. in bioinformatics, computational science or engineering, or a related discipline or equivalent experience and a minimum of 2 years related work experience or the equivalent combination of education and experience.

  • Demonstrated experience designing, developing, and testing quality software – preferably using Python in a UNIX/Linux environment.

  • Knowledge of software development practices – unit testing, self-documenting code, source code management (Git), bug tracking.

  • Excellent written and oral communications skills and the ability to collaborate and work as part of a large multidisciplinary team.

  • Ability to apply analytical skills and creativity to solve highly technical/complex problems.

  • Effective time management, organization, and planning skills with the ability to allocate resources and assign work to meet goals and deadlines.

  • Detail-oriented with the ability to work effectively in both team and solo environments.

In addition to the above, Data Scientist (Level 2) Required Qualifications:

  • A minimum of 5 years of related experience, or a Master's degree in Bioinformatics, Computer Science, Engineering, or closely related field and a minimum of 3 years related experience.

  • Experience with modern cluster/cloud/distributed computational and storage systems.

  • Demonstrated experience in bioinformatics and computational biology methods and tools for pairwise and multiple sequence alignment, profile search, protein clustering and phylogenetic analysis.

  • Familiarity with major concepts in recording of biochemical reactions and pathways, biological ontologies.

The posting shall remain open until the position is filled.

Notes:

  • This is a full time, 1 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.

  • 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.

Berkeley Lab (LBNL) 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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Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law."

 

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