In this exciting role, you will work as part of a team that develops software for key biological and bioinformatics resources including the Gene Ontology (GO), Open Biological Ontologies (OBO), the Monarch Initiative, and the National Microbiome Data Collaborative (NMDC).
You will build robust software and frameworks that support the creation and application of key bioinformatics knowledge bases. You will develop and maintain Python codebases and relational backends for modeling complex biological knowledge involving genes, gene function, causal biological networks, phenotypes, and diseases. You will work alongside domain scientists and bio curators to gather requirements and collaboratively build frameworks and tools. You will also work with data scientists engaged in cutting edge machine learning (ML) / artificial intelligence (AI) research that leverages these knowledge bases, and help them to operationalize information extraction pipelines and prediction tools.
This position will be hired at a Software Developer level 2 or 3. Level will be commensurate with the business needs and the skills, knowledge, and abilities of the successful candidate.
Level 2 Responsibilities:
Develop information systems for capturing and analyzing biological knowledge
Develop Python frameworks for accessing and storing data
Build workflows for scalable extraction, transformation, and loading of large biological databases
Work with an international team of software developers, curators, scientists, and clinicians to provide quality applications that realize scientific goals
Level 3 Responsibilities Also Include:
Help make biomedical data ML-ready
Work with domain experts to plan and prototype new applications, features, and interfaces
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
Level 2 Requirements:
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, or equivalent work experience
Experience using relational database management systems
Experience in team-based software engineering, using collaborative software development methodologies
Experience with modern devops workflows and implementations (e.g., Jenkins, GitHub actions)
Experience with cloud technologies
Experience with one or more data modeling frameworks (e.g., ER modeling, UML, JSON-Schema, LinkML)
Ability to work effectively both independently and in a diverse team environment
Level 3 Requirements Also Include:
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 6 years of relevant experience, or equivalent work experience
Demonstrated experience programming as part of a team on medium to large software applications
Demonstrated experience designing and deploying APIs using standards such as OpenAPI
Demonstrated experience working with users to gather requirements, demonstrate new features, etc.
Familiarity with biology and bioinformatics
Experience modeling and working with complex data (ideally biological)
Experience with developing UIs/front ends
Understanding of and experience with open-source software and open science
Experience with bioinformatics databases and resources
Experience with scalable workflows and pipelines
Level 3 Desired Qualifications:
Familiarity with semantic web standards, tools, and modeling frameworks (e.g., RDF, JSON-LD, SPARQL, SHACL)
Familiarity with biological ontologies (e.g., Gene Ontology, Human Phenotype Ontology, Environment Ontology) and ontology technologies and formats (OWL, OBO)
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.
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.
Work may be performed on-site, hybrid, or remote. Flexible work options are available. Work on-site will primarily be performed at West Berkeley Biocenter (Potter St.) -- Bldg. 977, 717 Potter St., Berkeley, CA.
Based on University of California Policy - SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit covid.lbl.gov for more information.
Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.
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.