Bioinformatics Programmer 3

Laboratory Medicine

Full Time

86634BR

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.

The final salary and offer components are subject to additional approvals based on UC policy.

Your placement within the salary range is dependent on a number of factors including your work experience and internal equity within this position classification at UCSF. For positions that are represented by a labor union, placement within the salary range will be guided by the rules in the collective bargaining agreement.

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

To learn more about the benefits of working at UCSF, including total compensation, please visit: https://ucnet.universityofcalifornia.edu/compensation-and-benefits/index.html

Department Description

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.

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

• Some experience in a computational biology, biology, or clinical lab
• Coding experience in the GO programming language (strongly preferred)
• Experience in working with clinical laboratory information management systems (LIMS)
• Familiarity with working in the Amazon EC2 cloud server environment
• Experience with routine lab hardware/software troubleshooting
• Experience with IT secure infrastructure (cloud or local) and highly regulated systems
• Familiar with AI and machine learning-based algorithms

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. We bring together the world's leading experts in nearly every area of health. We are home to five Nobel laureates who have advanced the understanding of cancer, neurodegenerative diseases, aging and stem cells.

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 - also known as our PRIDE values.

In addition to our PRIDE values, UCSF is committed to equity - both in how we deliver care as well as our workforce. We are committed to building a broadly diverse community, nurturing a culture that is welcoming and supportive, and engaging diverse ideas for the provision of culturally competent education, discovery, and patient care. Additional information about UCSF is available at diversity.ucsf.edu

Join us to find a rewarding career contributing to improving healthcare worldwide.

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.

Organization

Campus

Job Code and Payroll Title

009401 BIOINFORMATICS PROGR 3

Job Category

Clinical Systems / IT Professionals, Technical & Technologist

Bargaining Unit

99 - Policy-Covered (No Bargaining Unit)

Employee Class

Career

Percentage

100%

Location

San Francisco, CA

Campus

China Basin (SF)

Work Style

Fully On-Site

Shift

Days

Shift Length

8 Hours

Additional Shift Details

M-F, 40 hours/ week