Bioinformatics Software Developer

📁
Information Technology
💼
EB-Environ Genomics & Systems Bio
📅
94444 Requisition #

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

 

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)
  • Demonstrated software engineering skills. Strongly prefer experienced Python developers
  • 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.


Desired Qualifications:

  • 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)


Notes:

  • 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.

 

Equal Opportunity and IDEA Information Links:
Know your rights, click here for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. 

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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.

Equal Opportunity and IDEA Information Links:
Know your rights, click here for the supplement: "Equal Employment Opportunity is the Law." and the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4.

 

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The Lawrence Berkeley National Laboratory provides accommodation to otherwise qualified internal and external applicants who are disabled or become disabled and need assistance with the application process. Internal and external applicants that need such assistance may contact the Lawrence Berkeley National Laboratory to request accommodation by telephone at 510-486-7635, by email to eeoaa@lbl.gov or by U.S. mail at EEO/AA Office, One Cyclotron Road, MS90R-2121, Berkeley, CA 94720. These methods of contact have been put in place ONLY to be used by those internal and external applicants requesting accommodation.