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Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Core Research Software Engineer I - Integrated Genomics Core - **Company:** Other Staff - **Location:** San Diego, CA, United States - **Experience:** Starter - **Salary:** $68,640 - $79,040 - **Contract:** Internship / Graduate position - **Skills:** Microsoft Windows, Application Programming Interfaces (APIs), Artificial Intelligence, Amazon Web Services, User Authentication, Backup Devices, Big Data, Ubuntu (Operating System), CentOS, Command-Line Interface, Cloud Computing, Cloud Storage, Code Review, Continuous Delivery, Continuous Integration, Data Files, Software Debugging, Linux, Disaster Recovery, Django Web Framework, Github, Monitoring of Systems, Python (Programming Language), Linux System Administration, Open Source Technology, Red Hat Enterprise Linux, Svelte, Shell Script, Software Engineering, Software Systems, Web Application Frameworks, Backup and Restore, Scripting, Data Storage Management, Data Storage Technologies, High Performance Computing, ReactJS, Large Language Models, Claude Code, Reliability of Systems, AI Coding Agents, Backend, Git, Fastapi, Vue.js, Containerization, Kubernetes, Information Technology, Free and Open-Source Software, Slurm, Front End Software Development, Software Version Control, Docker - **Published:** November 10, 2026 - **Apply:** https://www.careerbuilder.com/job-details/core-research-software-engineer-i-integrated-genomics-core-la-jolla-ca--749ca64a-a7b8-443e-b60a-02a23c1d4343 ## About the Role Software Engineering, Genomics, Data Sets, Microscopy, Mass Spectrometry, Cloud Computing, Genomics, Facilities Management, Operational Support, Software Engineering, * 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., 2. A perception that the person has any of the characteristics or any combination of those characteristics. 3. 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. ## Description 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., * 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.