Staff Software Engineer, Instrument Control

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We are hiring a Staff Software Engineer to join our growing team. This role is central to the reliability of the instrument our customers depend on and to the architecture that will carry it forward. You will design and deliver the software that orchestrates our instrument’s hardware, from workflow execution and state management to integration with the cloud. As a technical leader, you will shape the evolution of our instrument software and raise the bar for how we build, test, and validate it. You will partner closely with peers across hardware, integration, bioinformatics, and biology teams to turn scientific workflows and customer needs into robust, well-designed software. Your strong technical judgment, communication, and leadership skills, as well as an eagerness to learn new domains, will have a meaningful impact on our team and the company on our path to the future. This position will report to the Senior Manager, Image Processing and is located in San Carlos, CA.

Here’s what you’ll be doing:

• You will own and implement core capabilities within our Instrument Control software stack. This will include hardware orchestration, instrument state management, workflow engine, and integration with other services both on-instrument and in the cloud.

• You will help guide the evolution of our instrument software architecture, bringing sound judgment to long-term decisions across the entire system. You will design everything from targeted improvements to ground-up redesigns, enabling our platform to scale to meet our future business needs.

• You will partner with engineering management to maintain a technical roadmap for our Instrument Control software.

• You will develop the technical skills of those around you by leading design reviews, holding a high bar for software quality, and mentoring others with a positive and empathetic attitude.

• You will bring genuine curiosity to the science behind the data, working alongside bioinformaticians, biologists, and product teams to deeply understand what our customers are trying to learn from their data and how our instrument’s behavior impacts their goals.

• You will join a tight-knit team of friendly people solving meaningful problems together.

We need to see:

• 7+ years of professional experience in a high-performing software engineering organization, plus a relevant 4-year degree or equivalent experience.

• Expertise with Python and C/C++.

• A strong track record of designing and delivering high-quality software that reliably operates and manages robotic devices, ideally in the biotechnology space.

• Expertise in software architecture. You know how to take an established codebase and make it more robust, reliable, and maintainable over time.

• Deep knowledge in concurrent / multithreaded programming.

• Experience working with Linux device drivers.

• Strength with CI/CD. You've built or maintained pipelines for automated testing, builds, and artifact management, and you know how to get code from commit to production.

• Excellent communication and cross-functional collaboration skills. You’re comfortable explaining software concepts to non-software audiences and building alignment from ambiguity.

• You care about the full lifecycle of what you build—design, testing, observability, and long-term maintainability—and have demonstrated it by shipping a product customers love.

• You’re excited to learn from others and develop skills outside of your typical area of expertise.

It’s a plus if:

• You have experience with databases and cloud services for Internet of Things (IoT) devices.

• You have delivered software to microcontrollers running an RTOS and know your way around low-level communication protocols (e.g., TCP/UDP, RS-232/422/485).• You have experience with optics and fluidics systems, particularly TDI cameras, hardware-controlled autofocus, pumps, and flow sensors.

• You have experience provisioning, securing, and maintaining Linux compute systems deployed in the field.

• You have worked in biotechnology and/or startups before.

Nautilus Team Culture

• We are curious go-getters: this is a team of life-long learners who aren’t afraid to tackle the big challenges while continuously pushing ourselves forward.

• We are detail oriented: we do great science by working smart and with diligence, and by learning from our mistakes.

• We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness.

Our Values

• Be Excellent

• Be a Good Human

• Catalyze Customer Success

• Dream Big

• Drive for Results

• Enjoy the Voyage

• Succeed as One Team