The Software Developer will help build applications and frameworks supporting a variety of high-profile bioinformatics projects and will contribute to a variety of critical National Institutes of Health (NIH) and Department of Energy (DOE) projects, including the Gene Ontology (GO), the Monarch Initiative, and the Center for Cancer Data Harmonization (CCDH).
This position involves developing and maintaining Python software for the creation, management, and analysis of biological knowledge about genes, pathways, diseases, and phenotypes. Working as part of a distributed team, the Software Developer will develop systems for interacting with databases (primarily graph/RDF databases), supporting curation interfaces, and workflow systems for integrating data from a variety of heterogeneous sources.
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 and medical informatics.
We encourage you to submit a cover letter with your application, and to include a URL for your code repository (e.g., GitHub or GitLab).
What You Will Do:
Work with an international team of software developers, curators, scientists, and clinicians to provide quality applications that realize scientific goals.
Work with domain experts to plan and prototype new applications, features, and interfaces.
Develop and maintain software for integrating biological data using ontologies.
Maintain and extend extract, transformation, and load pipelines.
Develop and maintain Python codebase for ontology-based data access.
Additional Responsibilities for Level 3:
Perform requirements analysis and work with product owners on software specifications.
Provide technical assistance and training to collaborators at other sites.
Serve as a key contributor to troubleshoot and solve highly technical, complex problems and provide direction for the project.
Assist in the writing of manuscripts and progress reports.
What is Required:
Bachelor's Degree in computer science, bioinformatics, or related field and a minimum of 5 years of relevant experience, or Master's Degree and a minimum of 3 years of relevant experience.
Demonstrated software engineering skills.
Experience in team-based software engineering, using collaborative software development methodologies.
Experience with one or more forms of database management systems (e.g., relational, graph, document).
Experience with the Python programming language.
Experience with modern devops workflows and implementations.
Experience with the maintenance and tuning of common software stacks.
Experience with one or more data modeling frameworks (e.g., UML, JSON-Schema, LinkML)
Ability to work effectively both independently and in a diverse team environment.
Knowledge of ontology and knowledge engineering frameworks, APIs, languages, and techniques (e.g., OWLAPI, Jena, SPARQL).
Experience with systems architecture, operations, deployment, and security.
Expertise with graph or RDF databases.
Understanding of and experience with open-source software and open science.
Familiarity with biomedical terminology.
Additional Desired Qualifications for Level 3:
Bachelor's Degree in computer science, bioinformatics, or related field and a minimum of 8 years of relevant experience, or Master's Degree and a minimum of 5 years of relevant experience.
Demonstrated experience programming as part of a team on mid to large software applications.
Demonstrated experience working with users to gather requirements, demonstrate new features, etc.
Experience modeling and working with complex heterogeneous biomedical data.
Demonstrated contributions to full stack applications for exploring, analyzing, or visualizing data.
This is a full time, 2 year, term appointment with the possibility of extension or conversion to Career
This position will be hired at a level commensurate with the business needs and the skills, knowledge, and abilities of the successful candidate.
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.
This position will be remote initially, but limited to individuals residing in the United States tentatively until 2022 due to COVID-19. Once the Bay Area shelter-in-place restrictions are lifted, work will be primarily performed at: West Berkeley Biocenter (Potter St.) -- Bldg. 977, 717 Potter St., Berkeley, CA. We are open to fully remote workers. The option fo remote work will also be available after shelter in place restrictions are lifted.
Learn about us!
Environmental Genomics and Systems Biology
Mission:Linking genome biology to ecosystem dynamics.
Vision: Sustainable solutions to energy and environmental challenges developed through mechanistic understanding of ecosystem dynamics.
Approach:We develop systems-level models using integrated molecular observation and controlled manipulation of model organisms and defined biomes to design and test interventions that promote beneficial outcomes.
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.
Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. To view information about the many rewards that are offered at Berkeley Lab- Click Here.
Internal Number: 92274
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.