Job:Software Developer: EB-Environ Genomics & Systems Bio
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2.2 years ago
BerkeleyLab ▴ 70

Software Developer - 92274

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.

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.

Desired Qualifications:

  • 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 for remote work will also be available after shelter in place restrictions are lifted.

How To Apply

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

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 (

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