Core Research Software Engineer I - Integrated Genomics Core

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Job Summary

The Salk Institute Core Facilities drive data-heavy biological research at the Salk Institute in multiple disciplines. The Core Facilities generate, manage and compute against large-scale datasets from genome sequencing, gene expression profiling, microscopy, spatial imaging, flow cytometry and mass spectrometry, using cloud and on-premise infrastructures.

The Salk Institute Core Facilities are looking for a Research Software Engineer to assist in daily systems administration and operational support for the technology infrastructure that underpins Salk’s data- and compute-intensive resource facilites, as well as core administrative services. This includes managing servers, storage, and instruments that enable biological research.

Your focus will be on the configuration, monitoring, and maintenance of Core systems and user services, ensuring they are secure, reliable, and optimized for performance.

Working under the general supervision of the Director of the Integrative Genomics Core, you will work in partnership with Salk Institute IT and the Center for AI and Research Computing (AIRC) personnel in assisting Core staff in implementing hardware and software solutions and supporting complex systems.

The role sits at the interface of research and software engineering, but it is grounded in the research side: unlike a conventional software engineer who builds to fixed product specifications, a Research Software Engineer works shoulder-to-shoulder with scientists to turn their evolving needs into working tools.

This position offers an opportunity to contribute directly to Salk’s scientific mission by maintaining robust Core Facilities services in a collaborative, mission-driven environment.

Who We Are

The Salk Institute is an internationally renowned research institution that values all (https://www.salk.edu/about/our-community/) members of our scientific community. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces perspectives across discipline, professional acumen, and unique life experiences, fostering innovation, and a sense of belonging.

Together, we strive to improve the wellbeing of humanity through groundbreaking research.

Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Salk's vibrant community has many talented individuals from varied backgrounds, each playing a crucial role in driving our mission forward.

From visionary leaders (https://www.salk.edu/about/management-team/) to dedicated administrators (https://www.salk.edu/administration/) and brilliant faculty members (https://www.salk.edu/science/directory/faculty/), the Institute is united by a shared passion for scientific exploration and innovation.

What Your Key Responsibilities Will Be

Systems Installations, Integrations, and Operations

• Develop, maintain, and release open-source scientific packages for core research purposes, following professional software engineering practices including version control (Git), code review, testing, type checking, and continuous integration/continuous deployment (CI/CD).
• Support and make use of shared high-performance computing resources, including GPU cluster scheduling and containerized job workflows (e.g., Kubernetes-based schedulers, SLURM).
• Rapidly prototype, build, and iterate on internal applications, command-line tools, and utilities in response to evolving scientific needs.
• Integrate systems and services through APIs, authentication, and automation to create seamless workflows for end users.
• Work directly with biologists and other scientists to understand their experimental goals and translate them into technical solutions.
• Prepare and maintain documentation, runbooks, and training materials that enable researchers to use the tools and pipelines independently.
• Contribute to the lab’s open-source software community, including reviewing external contributions and responding to user issues.
• Participate in project planning and status discussions, and coordinate with other Salk labs, Core facilities, and programs.
• Systems Monitoring & Maintenance: Monitor and maintain core facilities system health and capacity, and ensuring service reliability and uptime.
• OS Installation & Patching: Install and configure operating systems (primarily Linux/*NIX and Windows) on servers, workstations, and other Core Facility devices. Apply patches and updates to maintain security and optimize performance.
• Backups & Disaster Recovery: Execute backup and restore procedures for Core Facilty data, monitor backup jobs (on-premises and cloud) and remediate failures.
• Storage Management: Monitor Core Facility on premis and cloud storage usage. Address routine storage issues and performance or reliability concerns.

Technical Support and Additional Responsibilities

• Operational Support: Respond promptly to operational issues. Document resolution steps and follow-up actions for team knowledge sharing.
• Continuous Improvement: Identify and recommend opportunities to improve system reliability, performance, or efficiency. Contribute to Core Facility projects and initiatives, incorporating automation and innovative practices.
• Other Duties: Perform additional related duties as assigned, such as inventory management, procedure documentation, training new team members, or cross-training in other computational areas.
• Performs other related duties as assigned by management.

What we Require

QUALIFICATIONS:

• BS degree in computer science, engineering, quantitative science, or a related discipline is preferred for this position.
• Operating Systems: Strong proficiency with Linux server administration (such as Red Hat/CentOS or Ubuntu Linux), including shell scripting and command-line tools.
• Problem-Solving Skills: Strong analytical and troubleshooting skills to diagnose and resolve system issues efficiently. Capable of methodically isolating root causes in complex environments.
• Communication and Teamwork: Excellent verbal and written communication skills, with an ability to document processes and explain technical issues to non-technical audiences. A customer-service-oriented attitude is essential for working with researchers and staff. Proven ability to work both independently and collaboratively within a team, managing time effectively across multiple tasks.
• Full-stack software engineering ability, including proficiency in Python and at least one other language and experience building complete applications spanning back-end logic, front-end interfaces, and data storage.
• Fluency with modern, AI-assisted software development, including the effective use of AI coding tools and large language models (e.g., Claude Code) to design, build, debug, and ship software rapidly.
• Demonstrated ability to learn unfamiliar systems and technologies quickly and to stand up working services and pipelines through code, scripting, and automation.
• Comfort working in Linux/Unix environments with version control (Git), testing, and code review.

Preferred:

• Master’s degree or post-baccalaureate certification in a computational or scientific field.
• Prior internship, research, or work experience in a scientific, laboratory, or academic environment.
• Full-stack web development experience with modern frameworks (e.g., React, Svelte, Vue, FastAPI, Django).
• Experience integrating software with scientific instruments or hardware, such as cameras, scanners, or data-acquisition devices.
• Experience with containerization (e.g., Docker) and with scheduling work on GPU resources (e.g., Kubernetes, SLURM); prior high-performance computing or systems-administration experience is welcome but not required.
• Experience deploying and maintaining self-hosted applications and services, including on cloud platforms (e.g., AWS, GCP).
• Experience maintaining an open-source software project, including packaging, releases, and responding to community issues.
• Academic coursework, research experience, or demonstrated interest in plant science, biology, neuroscience, or another life-science domain.
• A track record of shipping small tools or projects quickly and independently, and of picking up new languages, frameworks, and systems with minimal ramp-up.
• Strong communication skills and the ability to work directly with scientists to translate their needs into technical solutions.
• A public code portfolio (e.g., GitHub) that demonstrates initiative beyond coursework, such as personal projects or contributions to open-source software.

What We Can Offer

The expected pay range for this position is $33.00-$38.00 hourly. 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, and external market pay for comparable jobs.

Benefits

• Salk Institute offers competitive benefits (https://www.salk.edu/about/careers/benefits/), including medical, dental, vision, retirement, paid time off, tuition reimbursement, patient advocacy services, and transit/parking program.
• Salk Values The Salk Community, both scientists and administrators, worked together to define values that we believe support Salk’s pursuit of excellence.
• To be truly the best scientific institution requires not only incredible discoveries, but a common understanding of how we should work together to enable those discoveries.
• The acronym “I CARE” (https://www.salk.edu/about/careers/values/) provides a simple way to remember each of the values and reminds each of us of the importance of what we do each day.

Equal Employment Opportunity

Statement

The Salk Institute for Biological Studies is an Equal Opportunity Employer and is committed to providing equal access to opportunities for students, employees, applicants for employment and other visitors. Salk has also adopted and maintains a policy to encourage professional and respectful workplace behavior and prevent discriminatory and harassing conduct in our workplace.

Accordingly, the Institute prohibits harassment and discrimination in employment on the basis of, and considers all qualified applicants for employment without regard to, actual or perceived race (race is inclusive of traits associated with race, including, but not limited to, hair texture and protective hairstyles.

Protective hairstyles include, but not limited to, such hairstyles as braids, and twists), color, religion, religious creed (including religious dress and grooming practices), national origin, ancestry, citizenship, physical or mental disability, medical condition (including cancer and genetic characteristics), genetic information, marital status, age, sex (including pregnancy, childbirth, breastfeeding, or related medical conditions), reproductive health decision making, gender, gender identity, gender expression, sexual orientation, veteran and/or military status (disabled veteran, veteran of the Vietnam era, other covered veteran status), political affiliation, and any other status protected by state or federal law.

Discrimination is prohibited with any intersectionality of the above-mentioned characteristics, including:

• Any combination of characteristics.
• A perception that the person has any of the characteristics or any combination of those characteristics.
• A perception that the person is associated with a person who has, or is perceived to have, any of those characteristics or any combination of those characteristics.

Equal Opportunity

Employer

This employer is required to notify all applicants of their rights pursuant to federal employment laws. For further information, please review the Know Your Rights (https://www.eeoc.gov/poster) notice from the Department of Labor.