Senior Instrument Engineer Jobs in California (NOW HIRING)

About the Role

We are seeking a Senior Automation Engineer to design, implement, and scale automated laboratory workflows and the supporting technologies that make them reliable, traceable, and extensible. This is a hands-on lab automation and technology development role focused on automating biological workflows on liquid handling robots and integrated automation workcells, while also developing the software, data, and LIMS-connected tools needed to make laboratory operations more scalable, observable, and AI-ready.

This role sits at the intersection of biology, automation, robotics, software, and data systems. You will translate scientific workflows into reliable automated processes, support production-scale execution, and help build the control layers, data interfaces, and system integrations needed for more adaptive laboratory operations.

Today, most lab automation systems are powerful but rigid, where hardware and software are typically designed to execute predefined instructions, not to understand workflow context, reason about errors, or support autonomous correction. This role will help close that gap by developing automation workflows and technical interfaces that connect physical lab systems with structured data, software tools, and future AI-enabled capabilities.

You will work closely with scientists, software engineers, data teams, robotics engineers, IT partners, vendors, and other engineering collaborators to develop practical automation systems that support both near-term execution and longer-term technology development.

This is an opportunity to help shape the foundation of modern, data-driven laboratory automation in a well-funded biotechnology environment.

Key Responsibilities

You will design, program, deploy, and support automated laboratory workflows using liquid handlers and integrated workcells, including platforms such as Hamilton liquid handlers and HighRes systems. This includes translating biological protocols into reliable automated methods, optimizing workflows for throughput and reproducibility, troubleshooting automation issues, maintaining automation platforms, and working with vendors or internal teams to expand system capabilities.

You will build and improve the software, data, and control interfaces that connect laboratory instruments, automation platforms, and informatics systems such as LIMS and ELN. This includes improving metadata capture, sample tracking, data traceability, structured APIs, instrument connectivity, and the flow of information between physical systems and downstream data infrastructure.

You will help develop tools that make lab automation more observable, adaptive, and AI-ready. This may include creating interfaces that allow software or AI-enabled systems to understand workflow state, interpret instrument outputs, detect errors, recommend corrective actions, or support more intelligent workflow execution under appropriate controls.

You will partner closely with scientists, software engineers, data teams, robotics engineers, IT partners, and external collaborators to identify automation opportunities and productionize workflows. Where relevant, this may include supporting robotic systems, material handling, computer vision, labware detection, quality control, and system monitoring within integrated laboratory workcells.

You will document protocols, system architecture, troubleshooting procedures, and best practices, while helping establish scalable automation standards for the organization. As a senior team member, you will also mentor junior engineers and help guide technical decisions across automation projects.

Required Qualifications

• Bachelor's or Master's degree in Engineering, Computer Science, Bioengineering or an automation related technical field.

• 5+ years of lab automation and 2+ years of hands-on experience with liquid handling platforms such as Hamilton, Tecan, Beckman, or similar systems.

• Experience designing, programming, deploying, and troubleshooting automated laboratory workflows in a research or production environment.

• Strong programming skills, preferably in Python and/or C#.

• Experience with laboratory data systems, including SQL, data modeling, metadata capture, and/or pipeline orchestration.

• Experience integrating automation systems with LIMS, ELN, or other laboratory informatics platforms.

• Experience connecting instruments or automation systems through APIs, middleware, IoT frameworks, or similar integration approaches.

• Strong troubleshooting skills and a systems-thinking mindset across hardware, software, data, and biological workflows.

• Ability to work effectively with scientists, engineers, software teams, data teams, vendors, and other cross-functional stakeholders.

Preferred Qualifications

• Experience with automation orchestration software such as Cellario, Momentum, Green Button Go, or similar platforms.

• Experience training, adapting, or evaluating AI/language models for tool use and real-world system interaction, including structured APIs, MCP-style connectors, software control layers, hardware interfaces, and agentic workflows.

• Experience or interest in computer vision for physical lab systems, including training or fine-tuning models for object detection, segmentation, pose estimation, labware detection, quality control, or monitoring applications using tools such as OpenCV, YOLO, SAM, or bounding-box/annotation workflows.

• Familiarity with molecular biology, cell biology, chemistry, or other wet-lab workflows.

• Experience with Benchling, AWS, cloud infrastructure, distributed systems, or modern data infrastructure.

• Experience mentoring junior engineers or helping establish automation best practices.

What We're Looking For

We are looking for a systems-oriented engineer who can connect laboratory hardware, software, data, and scientific workflows into reliable automation platforms. The ideal candidate has a builder mindset, strong ownership, and the ability to operate in a fast-moving, interdisciplinary environment.

This person should be excited by both hands-on lab automation and technology development. They should be comfortable programming liquid handlers, troubleshooting integrated work cells, building LIMS-connected tools, and working across software, data, robotics, and biology teams to create systems that are more reliable, observable, and extensible.

Compensation: Annual

We offer a competitive compensation and benefits package, seeking to provide an open, flexible, and friendly work environment to empower employees and provide them with a platform to develop their long-term careers. A Summary of Benefits is available for all applicants. We offer a competitive package that includes base salary, bonus, and equity.  The base pay range for this position is expected to be $152,000.00 - $190,000.00 annually; however, the base pay offered may vary depending on the market, job-related knowledge, skills and capabilities, and experience.
Xaira Therapeutics an equal-opportunity employer. We believe that our strength is in our differences. Our goal to build a diverse and inclusive team began on day one, and it will never end.
TO ALL RECRUITMENT AGENCIES: Xaira Therapeutics does not accept agency resumes. Please do not forward resumes to our jobs alias or employees. Xaira Therapeutics is not responsible for any fees related to unsolicited resumes.