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Job ID: 192216

Bioinformatics Programmer 2 (9402U), QB3 Institute - 40676
University of California, Berkeley

Date Posted Aug. 12, 2022
Title Bioinformatics Programmer 2 (9402U), QB3 Institute - 40676
University University of California, Berkeley
Berkeley, CA, United States
Application Deadline Open until filled
Position Start Date Available immediately
  • Professional Staff
  • Research/Technical/Laboratory

Bioinformatics Programmer 2 (9402U), QB3 Institute - 40676

About Berkeley

At the University of California, Berkeley, we are committed to creating a community that fosters equity of experience and opportunity, and ensures that students, faculty, and staff of all backgrounds feel safe, welcome and included. Our culture of openness, freedom and belonging make it a special place for students, faculty and staff.

The University of California, Berkeley, is one of the world's leading institutions of higher education, distinguished by its combination of internationally recognized academic and research excellence; the transformative opportunity it provides to a large and diverse student body; its public mission and commitment to equity and social justice; and its roots in the California experience, animated by such values as innovation, questioning the status quo, and respect for the environment and nature. Since its founding in 1868, Berkeley has fueled a perpetual renaissance, generating unparalleled intellectual, economic and social value in California, the United States and the world.

We are looking for equity-minded applicants who represent the full diversity of California and who demonstrate a sensitivity to and understanding of the diverse academic, socioeconomic, cultural, disability, gender identity, sexual orientation, and ethnic backgrounds present in our community. When you join the team at Berkeley, you can expect to be part of an inclusive, innovative and equity-focused community that approaches higher education as a matter of social justice that requires broad collaboration among faculty, staff, students and community partners. In deciding whether to apply for a position at Berkeley, you are strongly encouraged to consider whether your values align with our Guiding Values and Principles, our Principles of Community, and our Strategic Plan.

Departmental Overview

The California Institute for Quantitative Biosciences (QB3) is a cooperative effort between the state of California, private industry, venture capital, and the University of California campuses at Berkeley, San Francisco, and Santa Cruz. In order to stimulate discovery at the intersection of the physical and biological sciences, QB3 promotes multidisciplinary research at world-class facilities, creates innovative educational programs, and fosters industry partnerships. The Institute's more than 180 researchers decipher the complex systems involved in living systems and discover ground-breaking applications for that basic knowledge in the areas of health, energy, and the environment.

Application Review Date

The First Review Date for this job is: August 25, 2022.


Primary analysis of NGS data.

  • Process primary NGS data, including demultiplexing, file type conversion, and data organization.
  • Perform quality control analysis and assessment of NGS experiments.
  • Serve processed data to researchers.
  • Maintain computer systems in the GSL and FGL, including instrument-linked computers, core facility servers, data backup systems, and their associated networking.

Development of automation and analysis pipelines.

  • Develop automated pipelines, scripts, and utilities for use by CGRL, GSL, and FGL personnel.
  • Develop and operate analysis pipelines of NGS data as additional core services.
  • Provide limited custom analysis services to researchers on an hourly basis.

Manages organization, backups, and maintenance of systems for storing core facility-generated data.

  • Maintain backups of GSL data.
  • Establish, document, and maintain file organization of GSL and FGL systems.

Systems Administration

  • Coordinate with Berkeley Research Computing to provide technical support for CGRL's HPC resources.
  • Manage the CGRL user base.
  • In conjunction with Director/s, provide user management and technical support for the QB3 Genomics Laboratory Information Management system.
  • Coordinate with the GSL Systems Administrator to maintain and support the GSL's Linux systems.

Required Qualifications

  • Working knowledge of bioinformatics methods and NGS data.
  • Fluent with at least one high level scripting language (e.g. Python, R, Perl).
  • Familiarity with NGS technologies and methods.
  • Basic proficiency with shell scripting languages (e.g. BASH).
  • Proficiency with Linux/Unix systems.
  • Competency with the use and interpretation of common statistical methods.
  • Ability to present and communicate technical information in a clear and concise manner.
  • Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization.
  • Self-motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.
  • Bachelor's degree in related area and/or equivalent experience/training.

Preferred Qualifications

  • Advanced degree in related area and/or equivalent experience/training.

Salary & Benefits

This is a 100% full-time (40 hrs a week) non-exempt career position, which is paid bi-weekly and eligible for full UC Benefits. Hourly pay for this role is commensurate with experience within the range of $74,300.00 - $104,400.00.

For information on the comprehensive benefits package offered by the University visit:

How to Apply

Please submit your cover letter and resume when applying.

Equal Employment Opportunity

The University of California 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, or protected veteran status. For more information about your rights as an applicant see:
For the complete University of California nondiscrimination and affirmative action policy see:

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