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.
We have an exciting opportunity for a software developer with an interest in knowledge graphs, ontologies, and biocuration to help build applications and frameworks supporting a variety of high profile projects with high relevance for human and environmental health. The software developer will help build applications and frameworks supporting a variety of critical NIH and DOE projects, including the Gene Ontology (GO), the Monarch Initiative, and the new National Microbiome Data Collaborative (NMDC) project. The position will involve creating, evaluating and extending tools for ontology mapping, text mining, semantic search, and ontology-based analysis of a wide variety of datasets, including environmental and biomedical datasets.
We actively seek diverse applicants for this position. Note that applicants are not expected to have extensive knowledge of biology - we are open to those who are eager to learn about areas such as molecular biology, molecular ecology and microbiome science.
Working at Berkeley Lab offers many rewards, including excellent health insurance coverage, a retirement program that is second to none, outstanding employee development opportunities, and flexibility in work schedule. More information about the benefits of working at Berkeley Lab can be found at http://www.lbl.gov/HR/html/Employment/total-rewards.html.
Classification will depend upon the applicant's level of skills, knowledge, and abilities.
What You Will Do (Software Developer Level 2):
Evaluate and extend ontology mapping and text mining tools and deploy mapping/text mining pipelines for a variety of ontologies, including environmental, disease, and phenotype ontologies
Assist in the creation and development of data models and ontologies for structuring data, including environmental and biomedical sample data.
Develop systems for the automatic validation and QC of linked data, utilizing technologies such as ShEx and the biolink-model.
Prior experience working on a team that includes scientists as well as software developers
Prior experience working on collaborative projects involving multiple organizations and locations
Familiarity with bioinformatics tools and algorithms, in particular metagenomics analysis pipelines
Experience with knowledge representation frameworks, semantic web technology, shape languages such as ShEx, and APIs such as Jena/OWLAPI
Experience building ontologies or applying ontologies to bioinformatics analyses or text mining applications
Experience with workflow frameworks and continuous integration systems (e.g. CWL, nextflow, snakemake, Makefiles, Jenkins)
Some knowledge of molecular biology, molecular ecology and/or microbiome science.
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 the availability of funds and ongoing operational needs.
Classification will depend upon the applicant's level of skills, knowledge, and abilities. This position will be filled at the Software Developer Level 2 or Software Developer Level 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 West Berkeley Biocenter (Potter St.) -- Bldg. 977, 717 Potter St., Berkeley, CA.
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: 87704
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.