Job Description

Payroll Title:
San Diego Supercomputer Center
Hiring Pay Scale
$71,000 - $110,000 / Year
Appointment Type:
Appointment Percent:
Total Openings:
Work Schedule:
Days, 8 hrs/day, Mon - Fri

#114299 Scientific Software Developer

Extended Deadline: Wed 3/22/2023

UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply.

For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy

UCSD Layoff from Career Appointment: Apply by 02/01/22 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 02/11/22. Eligible Special Selection clients should contact their Disability Counselor for assistance.

Job posting will remain open until a suitable candidate has been identified.


As an Organized Research Unit of UC San Diego, the San Diego Supercomputer Center (SDSC) is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC launched Comet, a petascale supercomputer that joins the Center’s data-intensive Gordon cluster. SDSC is a partner in XSEDE (eXtreme Science and Engineering Discovery Environment), the most advanced collection of integrated digital resources and services in the world.

The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) of experimentally determined macromolecular structure information for research and teaching in biology, biological chemistry, and medicine. With unique users from over 160 countries around the world, the RCSB PDB is one of the leading worldwide Biological Databases. The RCSB PDB is funded by a consortium involving the National Science Foundation, the Department of Energy, and various of the National Institutes of Health, to ensure facile, open access to a secure, singular experimental data archive of macromolecular structural biology that will be maintained in perpetuity for the public good.

The Scientific Software Developer will use his/her skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms; identify and resolve a wide range of issues/software bugs. S/he will demonstrate good judgment in selecting methods and techniques for obtaining solutions and operate independently.

The incumbent will develop, implement, and maintain complex scientific and web-based software systems for the RCSB Protein Data Bank (PDB; at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively with other software developers and scientists at the San Diego Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand's functionality and reliability as a premier biological data and information resource. Also, s/he will develop new scalable algorithms for the mining and analysis of the rapidly growing PDB archive and computed models databases using leading edge Big Data technologies. Additionally, the incumbent will design and implement user interfaces for the query, analysis, reporting, and visualization of 3D structural information and associated annotations; integrate external database resources with RCSB PDB to provide a structural view of biology; as well as help lead the design of databases and data warehouses to store and aid in the query of data. Be actively involved in the software development process, maintenance and system standards for analysis algorithms, tools, and infrastructure.

The incumbent will serve as an expert on relevant scientific and technical aspects of the various web, web services, and database components of the RCSB PDB, stay abreast of the latest development in structural and computational biology and new technologies, and apply advanced bioinformatics concepts to design, develop, modify, debug, and evaluate highly complex software programs and web tools. S/he will also translate scientific problems into scalable and maintainable software solutions that meet end-user needs and further science through Scientific Publications, written in collaboration with our team.

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  • Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training. Advanced Degree in Bioinformatics, Biology, Chemistry, Computer Science, or a similar field and / or equivalent experience / training preferred.

  • Thorough knowledge of bioinformatics methods, applications programming, web development and data structures. Proven experience with Workflows, Automation, Microservice, Algorithms, and Data Structures.

  • Thorough knowledge of bioinformatics programming design, modification and implementation. Proven experience with languages such as: Java, Python, Javascript.

  • Understanding of relational databases, web interfaces, and operating systems. Proven experience with Cloud Services and Cloud Native Designs, Docker, Relational Database, Object Database, MySQL, MongoDB, SOLR, Elastic Search, REST service design, GraphQL and Git.

  • Demonstrated knowledge of modern biology and applicable field of research.

  • Proven vision in discovering/defining/publishing new methods to support Bioinformatics data standards, tools, algorithms and/or data structures.


  • Job offer is contingent upon satisfactory clearance based on Background Check results.

Pay Transparency Act

Annual Full Pay Range: $71,000 - $160,000 (will be prorated if the appointment percentage is less than 100%)

Hourly Equivalent: $34.00 - $76.63

Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable).

Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral).

To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community.

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, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see:

UC San Diego is a smoke and tobacco free environment. Please visit for more information.

Application Instructions

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