Bioinformatics Programmer 3

Job Summary

This is a 100% full‑time position, divided into 50% research and 50% clinical laboratory (UCSF Laboratory Information Systems) efforts. The Chiu laboratory at University of California, San Francisco has developed and validated clinical metagenomic next‑generation sequencing assays (mNGS) for diagnosis of infectious diseases. Currently, the CLIA‑certified UCSF Clinical Microbiology Laboratory is running CSF and plasma mNGS assays for patients at UCSF Medical Center and across the broader University of California Health system.

We are seeking a computational analyst with relevant experience to maintain and develop the clinical workflow software for these assays, the UCSF SURPI+ (sequence‑based ultra‑rapid pathogen identification) computational pipeline, and the associated websites to usher in the next generation of computational tools for pathogen detection from clinical samples.

Half of the candidate’s effort will be devoted to monitoring and maintaining the automated metagenomics (mNGS) testing workflow that supports the analysis and display of clinical sequencing data. The mNGS tests run on a hybrid infrastructure consisting of on‑premises virtual servers and cloud‑based data storage and computation using Amazon Web Services (AWS). Duties include maintaining and updating clinical servers and associated software for data processing, relational database management, and pipeline development / execution, as well as troubleshooting problems arising during the workflow or analyses.

The candidate will also be working closely with researchers and bioinformaticists in the UCSF Chiu laboratory. Research in the Chiu laboratory focuses on the development of sequencing‑based assays for pathogen detection and host response profiling in clinical samples. The remaining half of the candidate’s effort will be working on translational research projects in the Chiu laboratory, which will mostly focus on (1) enhancing SURPI+ by adding features such as host response profiling analyses and pathogen load calculations, (2) modifications to the web‑based interface and automated result reports from the clinical analyses, (3) writing programs for analysis of large clinical sequencing datasets, and (4) maintaining and updating research servers and associated software for data processing, relational database management, and pipeline development / execution.

The candidate must have prior experience in software development, preferably clinical, and Linux server administration. Preferred qualifications would be familiarity with AWS, laboratory information management systems (LIMS) such as Beaker and EPIC (UCSF APeX), the Go programming language, BASH shell scripting, and Python programming.

Certain terms and conditions of employment for this position, including the rate of pay, benefits, etc are currently subject to negotiation with the appropriate union.

To learn more about the benefits of working at UCSF, including total compensation, please visit : UCSF Compensation & Benefits

Salary Range

The salary range for this position is $108,200 – $162,200 (Annual Rate).

Required Qualifications

• BA / BS / MS or PhD in computer science, bioinformatics, or related field
• At least one year of basic biology knowledge
• Computer science and / or bioinformatics with familiarity with coding in a Linux environment (shell scripting and Python)
• Excellent organizational, communication, and interpersonal skills
• Experience in server maintenance (hardware and software)

Preferred Qualifications

About UCSF

The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate‑level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10‑campus UC system dedicated exclusively to the health sciences.

PRIDE Values

UCSF is a diverse community made of people with many skills and talents. We seek candidates whose work experience or community service has prepared them to contribute to our commitment to professionalism, respect, integrity, diversity, and excellence — the PRIDE values. In addition to our PRIDE values, UCSF is committed to equity in how we deliver care and as a workforce.

Equal Employment Opportunity

The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law.

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