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Software Developer

Lawrence Berkeley National Laboratory
Job Location
717 Potter St
Berkeley, CA 94710
United States
Job Description

Software Developer - 91411

Organization: EB-Environ Genomics & Systems Bio


Lawrence Berkeley National Lab (LBNL,’s Environmental Genomics and Systems Biology Division ( has an opening for a Software Developer to join the team.


In this exciting role the Software Developer will help build applications and frameworks supporting a variety of high-profile bioinformatics projects. The Software Developer will contribute to a variety of critical NIH and DOE projects, including the Gene Ontology (GO), the Monarch Initiative, the National Microbiome Data Collaborative (NMDC), and the Center for Cancer Data Harmonization (CCDH).


As a Software Developer in our group, you will develop and maintain robust software for the creation, management, and utilization of ontologies and knowledge graphs for applications in systems biology, human health, and environmental microbiology. Working as part of a distributed team, you 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. This position involves interacting with users (including a range of biomedical scientists and biocurators). This position will be hired at a level 2 or 3 contingent upon level of experience, skills, knowledge, and abilities of the successful candidate.



• 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.

• This position will initially be remote, but limited to individuals residing in the United States tentatively until 2021 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. Full remote work is also available.



What You Will Do:

• 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.


In addition to the above, Specific Responsibilities for a 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.


What is Required for a Level 2:

Bachelor’s Degree and/or equivalent experience 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

• Experience with one or more forms of database management system (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.

• Excellent software engineering skills.

• Ability to work effectively both independently and in a diverse team environment.


In addition to the above, Required Qualifications for Level 3:

Minimum of 8 years of relevant experience with a Bachelor’s Degree or 6 years with a Master’s.

• Experience with one or more data modeling frameworks (e.g. UML, JSON-Schema, Biolinkml)

• Experience with full stack development.


Desired Qualifications for both levels:

• Knowledge of ontology and knowledge engineering frameworks, APIs, languages, and techniques (e.g., OWLAPI, Jena, SPARQL).

• Experience modeling and working with complex data (ideally biological).

• Expertise with graph or RDF databases.

• Experience with systems architecture, operations, deployment, and security.

• Understanding of and experience with open source software and open science.


How to Apply

How To Apply

Apply directly online at and follow the on-line instructions to complete the application process.

About Our Organization

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

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 (


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.


Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers.


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