Computer Systems Engineer, Software Developer

Job title: Computer Systems Engineer, Software Developer

Company: Berkeley Lab

Job description: Lawrence Berkeley National Lab’s ( ) Joint Genome Institute ( ) Division has an opening for a Software Developer to join the Genomes Online Database ( ) team.

The Genomes Online Database (GOLD) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. GOLD metadata management system supports the metadata curation for the projects carried out at the JGI and facilitates their annotation in the Integrated Microbial Genome (IMG) system. GOLD also supports submitting JGI generated data to public repositories by registering BioProject and BioSamples at NCBI. To maintain an up-to-date reference dataset for comparative analysis by JGI users, PIs, and science programs, GOLD imports projects from public repositories like GenBank, curates metadata and facilitates their annotation in IMG.

In this exciting role, you will work on the development of tools to support and work in an interdisciplinary environment in close collaboration with biologists, engineers and computer scientists to develop both back end and user facing web interface of GOLD. You are expected to update and inform appropriate leadership, stakeholders, and champions when critical junctures are reached.

What You Will Do:

  • Development of metadata storage, web resource and analysis systems at the GOLD.
  • Set up and manage Java-related systems, web services, and scripts (both stand-alone and web-based) for collecting, storing, and editing metadata, from internal and public sources.
  • Develop automated quality control scripts; improve data-mining and data-import pipelines.
  • Develop user interface for large scale metadata-based comparative analysis.
  • Add support to local (existing and new) systems for GSC (Genomic Standards Consortium) environmental packages.
  • Develop data warehouse metadata statistics and add support for historical data.
  • Support JGI’s Data Science and Informatics department’s projects and initiatives encompassing metadata from GOLD.
  • Work in close collaboration with National Microbiome Data Collaborative (NMDC) on projects related to metadata curation as wells as metadata exchange between GOLD and NMDC.
  • Develop and present updates and reports at group meetings.
  • Participate in the preparation of publications.

Additional Responsibilities as needed:

  • Communicate easily with scientific staff and end-users to gather software specifications and requirements.
  • Ability to evaluate and design new software-based solutions.

What is Required:

  • A minimum of 2 years of related experience with a Bachelor’s degree; or an advanced degree without experience; or equivalent work experience.
  • Degree in Biology, Computer Science, Bioinformatics, or a related field.
  • Demonstrated experience in using Java, Python, Oracle (or PostgreSQL), SQL, JSP, JavaScript (including at least one JS framework, like jQuery or Node.js), HTML / CSS, Web services (JSON and XML), Hibernate ORM (or other JPA implementation and Unix/Linux.
  • Familiarity with (or interest in) molecular biology, comparative genomics, metagenomics, and microbial ecology.
  • Strong problem-solving, decision-making, and analytical skills, to make sound judgments and recommend creative solutions to moderately complex problems.
  • Strong interpersonal skills, to work with scientific and administrative customers to define needs and priorities.
  • Ability to troubleshoot complex systems and data analysis problems.

Desired Qualifications:

  • Demonstrated experience utilizing disciplined and modern coding habits, such as unit testing (ideally Junit, Selenium, or other framework), dependency injection (Guice or Spring DI), self-documenting code, etc.
  • Prior experience processing and analyzing genomic and genetic data.
  • Prior experience in working with biological databases or public repositories like GenBank and other NCBI systems is a plus.
  • Agile programming, Test-driven development, and Jenkins automation server.
  • Experience in Bash/shell scripting, Vi (or other Unix-based text editor), Apache Tomcat server administration (or other Java web server), Apache Lucene-based search engine (e.g. Hibernate Search, Solr, Elastic search), Apache Maven (or Gradle) NoSQL and Git.
  • Experience in User Interface (UI) development.


  • This is a full time, 1 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 will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

Learn About Us:

JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest

They say it’s all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class multidisciplinary science within a diverse and respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Genome Institute (JGI) addresses the most pressing energy and environmental challenges using integrative genome science approaches. JGI takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of our next ground-breaking discoveries?

(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- .

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 under 41 CFR 60-1.4. Click 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.

Expected salary:

Location: California

Job date: Thu, 18 Feb 2021 07:01:05 GMT

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