Staff Software Engineer, Instrument Control

Nautilus Biotechnology • San Carlos, CA

4d • $193,000 - $277,000 • Onsite

About The Position

Nautilus is hiring a Staff Software Engineer to build and evolve the Instrument Control software that orchestrates its single-molecule protein analysis instrument. The role is central to instrument reliability and software architecture, covering hardware orchestration, instrument state management, workflow execution, and integration with services on the instrument and in the cloud. The engineer will help shape the software architecture and technical roadmap, make long-term system decisions, and improve how the software is built, tested, and validated. They will collaborate with teams across hardware, integration, bioinformatics, biology, product, and engineering management to translate scientific workflows and customer needs into robust software. The role also includes technical leadership through design reviews, software quality practices, and mentoring. The position reports to the Senior Manager, Image Processing and is located in San Carlos, California.

Requirements

• At least 7 years of professional experience in a high-performing software engineering organization, plus a relevant four-year degree or equivalent experience.
• Expertise in Python and C/C++.
• A strong track record of designing and delivering high-quality software that reliably operates and manages robotic devices.
• Expertise in software architecture and the ability to improve an established codebase's robustness, reliability, and maintainability.
• Deep knowledge of concurrent and multithreaded programming.
• Experience working with Linux device drivers.
• Strength with CI/CD, including building or maintaining pipelines for automated testing, builds, and artifact management, and delivering code from commit to production.
• Excellent communication and cross-functional collaboration skills, including explaining software concepts to non-software audiences and building alignment amid ambiguity.
• Commitment to the full lifecycle of software, including design, testing, observability, and long-term maintainability, demonstrated by shipping a product customers love.
• Eagerness to learn from others and develop skills outside one's typical area of expertise.

Nice To Haves

• Experience with databases and cloud services for IoT devices.
• Experience delivering software to microcontrollers running an RTOS and familiarity with low-level communication protocols such as TCP/UDP and RS-232/422/485.
• Experience with optics and fluidics systems, particularly TDI cameras, hardware-controlled autofocus, pumps, and flow sensors.
• Experience provisioning, securing, and maintaining Linux compute systems deployed in the field.
• Experience in biotechnology and/or startups.

Responsibilities

• Own and implement core capabilities in the Instrument Control software stack, including hardware orchestration, instrument state management, workflow engine, and integration with on-instrument and cloud services.
• Guide the evolution of instrument software architecture and make sound long-term system decisions, including targeted improvements and ground-up redesigns.
• Partner with engineering management to maintain a technical roadmap for Instrument Control software.
• Lead design reviews, uphold a high bar for software quality, and mentor colleagues with a positive and empathetic approach.
• Work with bioinformaticians, biologists, and product teams to understand scientific and customer goals and how instrument behavior affects them.
• Collaborate with peers across hardware, integration, bioinformatics, and biology to turn scientific workflows and customer needs into robust software.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior