TheDepartment 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.
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.
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."
Internal Number: 86097
About Lawrence Berkeley National Laboratory
In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with excellence. Thirteen scientists associated with Berkeley Lab have won the Nobel Prize. Fifty-seven Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation's highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world. Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular... views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2011 is $735 million, with an additional $101 million in funding from the American Recovery and Reinvestment Act, for a total of $836 million. A recent study estimates the Laboratory's overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars. Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence's belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.