Scientific Software Developer

University of California San Diego
San Diego Supercomputer Center (SDSC)/The Research Collaboratory for Structural Bioinformatics (RCSB)/Protein Data Bank (PDB)
United States CA 92093


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 incumbent 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. S/he will develop new scalable algorithms for the mining and analysis of the rapidly growing PDB archive using leading edge Big Data technologies, design and implement user interfaces for the query, analysis, reporting, and visualization of 3D structural information and associated annotations, as well as integrate external database resources with RCSB PDB to provide a structural view of biology. The incumbent will help lead the design of databases and data warehouses to store and aid in the query of data and be actively involved in the software development process, maintenance and system standards for analysis algorithms, tools, and infrastructure.

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


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.

Strong communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization.

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

Job offer is contingent upon a satisfactory clearance based on background check results.

Start date

As soon as possible

How to Apply

Please submit resume and application to by visiting the following link:

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