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Research Software Engineer, Department of Cores

Salk Institute for Biological Studies
La Jolla, CA

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Job Details

The Research Computing Service group will participate in the development of  high-quality and sustainable research software with broad impact across the Salk Institute.  This position will be an integral member of multiple projects collaborating with Salk researchers to provide computational expertise in algorithm development and software design to create high-quality and sustainable research code.


  • Lead the design and construction of complex research software systems needed to acquire, process, and analyze data from biological experiments. 
  • Establish a set of best practices that are appropriate for each project (e.g version control, continuous integration, continuous delivery, software design, programming model, etc.), and enable long-term maintainability and sustainability by documenting projects in an appropriately detailed manner. 
  • Respond to evolving research needs and apply research software engineering experience to develop robust software solutions to solve challenging research problems. Port, debug, tune and potentially parallelize existing research code to meet criteria set by the research team.
  • Transfer knowledge, expertise, and methodologies by providing technical assistance and mentorship to reseachers, including graduate students and postdoctoral fellows. 
  • Independently or in collaboration with a team, develop scope and project management plans, meet milestone delivery timelines, and communicate with the research team. Communicate software engineering concepts with project teams consisting of domain experts with varying degrees of software engineering knowledge.
  • Apply appropriate domain-specific algorithms, techniques, and code to advance software engineering. 
  • Initiate and/or maintain open collaboration with Salk researchers as needed.  Regularly meet with, listen to, and ask questions of the relevant collaborators for active projects. Understand and address software engineering questions that arise in research planning. 
  • Through independent research (reading publications, etc.) and/or studying existing code bases understand the necessary elements of biological research to converse with Salk researchers
  • Maintain and expand knowledge of current and future software development tools and techniques, programming languages, and computing hardware.
  • Perform other related duties as assigned by management.


  • This job has no supervisory responsibilities.


  • Bachelor's Degree (BA) from four-year college or university, plus five (5) years of related experience and/or training, or equivalent combination of education and experience required.
  • Specific experience required: exposure to research, numerical computing, high performance computing
  • Programming language skills required: Python, R, C++, Bash.
  • Experience with containerization and cloud-native technologies (Docker & Kubernetes) required.
  • Other skills required: DevOps (version control, CI/CD, compilation toolchains, documentation generation), familiarity with cloud platforms (GCP, AWS, or Azure)

Preferred Qualifications

  • Experience with web development languages and frameworks (HTML5, Node.js, Angular/React/Vue, Canvas, WebAssembly)
  • Deep learning experience (familiarity with PyTorch, TensorFlow and/or Jax)
  • GPU programming experience (e.g., CUDA, OpenCL) and/or experience with FPGAs 
  • Parallel programming expertise (e.g., OpenMP, Kokkos, etc.) 
  • Experience developing scientific software with significant emphasis on performance 
  • Experience developing research software outside of core domain knowledge 
  • Academic research experience. 
  • A Master’s/Ph.D. in computer science, or other applied domain sciences (esp. natural sciences) with a strong computational focus is strongly preferred.


  • Adaptability - Adapts to changes in the work environment; Manages competing demands; Changes approach or method to best fit the situation; Able to deal with frequent change, delays, or unexpected events.
  • Design - Generates creative solutions; Translates concepts and information into images; Uses feedback to modify designs; Applies design principles; Demonstrates attention to detail.
  • Innovation - Displays original thinking and creativity; Meets challenges with resourcefulness; Generates suggestions for improving work; Develops innovative approaches and ideas; Presents ideas and information in a manner that gets others' attention.
  • Oral Communication - Speaks clearly and persuasively in positive or negative situations; Listens and gets clarification; Responds well to questions; Demonstrates group presentation skills; Participates in meetings.
  • Problem Solving - Identifies and resolves problems in a timely manner; Gathers and analyzes information skillfully; Develops alternative solutions; Works well in group problem solving situations; Uses reason even when dealing with emotional topics.
  • Project Management - Develops project plans; Coordinates projects; Communicates changes and progress; Completes projects on time and budget; Manages project team activities.
  • Teamwork - Balances team and individual responsibilities; Exhibits objectivity and openness to others' views; Gives and welcomes feedback; Contributes to building a positive team spirit; Puts success of team above own interests; Able to build morale and group commitments to goals and objectives; Supports everyone's efforts to succeed.
  • Technical Skills - Assesses own strengths and weaknesses; Pursues training and development opportunities; Strives to continuously build knowledge and skills; Shares expertise with others.
  • Ethics - Treats people with respect; Keeps commitments; Inspires the trust of others; Works with integrity and ethically; Upholds organizational values.

The expected pay range for this position is $82,000 - $110,000 per annum.
Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.


  • Frequently/Continually required to sit at a computer
  • Frequently/Continually required to utilize hand and finger dexterity
  • While performing the duties of this job, the noise level in the work environment is usually quiet
  • The employee must occasionally lift and /or move up to 5 pounds

The above is intended to describe the general content of and requirements for the performance of this job.  It is not to be construed as an exhaustive statement of duties, responsibilities or physical requirements.  Nothing in this job description restricts management’s right to assign or reassign duties and responsibilities to this job at any time. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

The Salk Institute is an internationally renowned research institution that values diversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.


Working at Salk Institute for Biological Studies

The Salk Institute for Biological Studies is one of the world's preeminent basic research institutions, where internationally renowned faculty probe fundamental life science questions in a unique, collaborative, and creative environment. Focused on both discovery and mentoring future generations of researchers, Salk scientists make groundbreaking contributions to our understanding of cancer, aging, Alzheimer's, diabetes, and cardiovascular disorders by studying neuroscience, genetics, cell and plant biology, and related disciplines.

Faculty achievements have been recognized with numerous honors, including Nobel Prizes and memberships in the National Academy of Sciences. Founded in 1960 by polio vaccine pioneer Jonas Salk, M.D., the Institute is an independent nonprofit organization and architectural landmark.

Salk Equal Opportunity and Non-Discrimination Statement

The Salk Institute for Biological Studies is committed to providing equal access to opportunities for students, employees, applicants for employment and other persons.

Our policies prohibit harassment or unlawful discrimination against individuals on the basis of sex, gender, marital or parental status, pregnancy, childbirth, breastfeeding, medical conditions/disabilities related to pregnancy, childbirth or breastfeeding, gender identity, gender expression, or sexual orientation age, ancestry, color, religion (including religious dress and grooming practices), family and/or medical care leave status, disability (mental or physical), registered domestic partner status, legally protected medical condition, genetic information, military or veteran status (disabled veteran, veteran of the Vietnam era, other covered veteran status), national origin (including language use restrictions and possession of a driver’s license), race, religion or any other classification protected by local, state or federal laws.

The Salk Institute participates in the E-Verify program.

Reasonable accommodation is available for qualified individuals with disabilities and for individuals with religious restrictions.

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