Software Developer (Genomics Analysis Team) at Lawrence Berkeley National Laboratory

Berkeley, California, United States -

Full Time

Start Date

Immediate

Expiry Date

08 Jun, 26

Salary

197676.0

Posted On

10 Mar, 26

Experience

5 year(s) or above

Remote Job

Yes

Telecommute

Yes

Sponsor Visa

Skills

Python, Pandas, Matplotlib, FastAPI, MySQL, PostgreSQL, Unix, Git, BASH/Shell Scripting, HTML, CSS, JavaScript, Relational Databases, Data Visualization, Pipeline Monitoring, Troubleshooting

Industry

Research Services

Description

Berkeley Lab’s (LBNL) Joint Genome Institute (JGI) has an opening for a Software Developer to join the Genomics Analysis Team! In this exciting role, you will support the development, maintenance, and optimization of critical infrastructure supporting large-scale genomics research. This role focuses on supporting the automation of a diverse set of genome analysis pipelines and their associated quality control processes. It is central to building the Institute’s analytical capabilities, enabling growth from processing tens to hundreds of thousands of samples in support of exciting, large-scale scientific initiatives. This hands-on role involves building and maintaining next-generation sequencing (NGS) data processing pipelines, designing relational databases for genomics data, and creating internal web applications for data visualization and pipeline monitoring. You will work with a substantial existing codebase, learning complex systems while adding new functionality based on scientific and operational requirements. You will troubleshoot production systems, optimize database performance and queries, support ad-hoc analyses for research staff, and produce clear, high-quality technical documentation. The JGI’s mission is to provide the global research community with access to the most advanced integrative genome science capabilities in support of the DOEs research mission to solve the world’s evolving energy and environmental challenges. The JGI supports projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. This position is headquartered on the Lab’s main site at the Integrative Genomics Building (IGB) (Virtual Tour). This position has an anticipated start date of April 13, 2026. We’re here for the same mission, to bring science solutions to the world. Join our team and YOU will play a supporting role in our goal to address global challenges! Have a high level of impact and work for an organization associated with 17 Nobel Prizes! Why join Berkeley Lab? We invest in our employees by offering a total rewards package you can count on: Exceptional health and retirement benefits, including pension or 401K-style plans A culture where you’ll belong - we are invested in our teams! In addition to accruing vacation and sick time, we also have a Winter Holiday Shutdown every year. Parental bonding leave (for both mothers and fathers) Pet insurance What You Will Do: Troubleshoot complex systems and monitor performance across production data pipelines. Develop and maintain pipelines for processing next-generation sequencing (NGS) data. Design and maintain relational databases supporting large-scale genomics data. Build and maintain internal web applications for data visualization and pipeline monitoring. Maintain and enhance a substantial codebase (Python) distributed across several code repositories. Implement new functionality based on evolving scientific and operational requirements. Produce high-quality documentation for software systems and analytical approaches. Provide technical support for ad-hoc genomic analyses in collaboration with scientific staff. What is Required: A Bachelor’s Degree (or equivalent knowledge/training) in Operations Research, Systems Engineering, Computer Science, or a related discipline and a minimum of 5 years of professional software engineering experience in industry or production environments or an equivalent combination of education and experience. Demonstrated capacity to manage multiple projects and competing priorities. Strong proficiency in Python using pandas, matplotlib, data processing libraries, and RESTful web service development with FastAPI. Experience with relational databases (MySQL/PostgreSQL) in Unix environments, including query optimization and schema design. Hands-on experience with Git workflows, proficiency in BASH/shell scripting for automation, and an ability to create dynamic web pages using HTML, CSS, and JavaScript. Demonstrated track record of maintaining and evolving complex codebases. Strong analytical skills including the ability to identify problems, troubleshoot, and demonstrate good judgement in selecting methods and techniques for obtaining solutions. Excellent oral and written communication skills, including experience organizing and presenting technical information to varying audiences. Demonstrated interpersonal skills including experience collaborating with an interdisciplinary research team. Desired Qualifications: Experience with CI/CD pipelines and automated testing. Experience with Linux system administration with containerization technologies (Docker, Singularity). Experience with HPC computing environments and job schedulers (SLURM). Hands-on experience with cloud platforms (AWS, GCP, or Azure). Familiarity with workflow management systems (Snakemake, Nextflow, Cromwell). Familiarity with NGS platforms (Illumina, PacBio, Oxford Nanopore). Experience applying machine learning, pattern recognition, or modeling techniques to scientific problems. Additional Information: Application Date: Priority consideration will be given to candidates who apply with a resume and cover letter describing interest in this position by March 23, 2026. Applications will be accepted until the job posting is removed. Appointment Type: This is a full time, exempt from overtime pay (monthly paid), 2 year (benefits eligible), 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. Salary Information: This position has a budgeted salary range of $117,132 - $146,400 annually, which fits within the full salary range of $117,132 - $197,676 annually for job code C70.2. It is not typical for an individual to be offered a salary at or near the top of the range for a position. Salary will be commensurate with the final candidate’s qualification and experience, including skills, knowledge, relevant education, certifications, and aligned with the internal peer group. Background Check: This position is 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 Modality: This position will be performed onsite at Lawrence Berkeley National Lab located at 1 Cyclotron Road, Berkeley, CA 94720. Work schedules are dependent on business needs. A REAL ID or other acceptable form of identification is required to access Berkeley Lab sites (for more information click here). Relocation Assistance: This position is eligible for relocation assistance. Work Authorization: Applicants must be legally authorized to work in the United States. Berkeley Lab does not provide visa sponsorship for this position. Want to learn more about working at Berkeley Lab? Please visit: careers.lbl.gov Equal Employment Opportunity Employer: The foundation of Berkeley Lab is our Stewardship Values: Team Science, Service, Trust, Innovation, and Respect; and we strive to build community with these shared values and commitments. Berkeley Lab is an Equal Opportunity Employer. We heartily welcome applications from all who could contribute to the Lab's mission of leading scientific discovery, excellence, and professionalism. In support of our rich 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, protected veteran status, or other protected categories under State and Federal law. Berkeley Lab is a University of California employer. It is the policy of the University of California to undertake affirmative action and anti-discrimination efforts, consistent with its obligations as a Federal and State contractor. Misconduct Disclosure Requirement: As a condition of employment, the finalist will be required to disclose if they are subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct, are currently being investigated for misconduct, left a position during an investigation for alleged misconduct, or have filed an appeal with a previous employer.

Responsibilities

The role involves developing, maintaining, and optimizing critical infrastructure for large-scale genomics research, focusing on automating genome analysis pipelines and quality control processes. Key tasks include building next-generation sequencing data processing pipelines, designing relational databases, and creating internal web applications for monitoring and visualization.