FL97 | Cambridge, MA Principal Automation Engineer, Workcell Builds

Flagship Pioneering; Cambridge (MA); On-site; USD 80,000 - 150,000; Full time

Job summary

Join a mission-driven team at a pioneering company that is transforming science through AI and automation. As a Principal Automation Engineer, you will lead the design and deployment of innovative automation systems that bridge life sciences and material sciences. This role offers the opportunity to create scalable solutions, implement advanced error recovery protocols, and drive innovation in custom hardware development. Collaborate with cross-functional teams to optimize workflows and enhance research capabilities. If you are passionate about leveraging technology to make a significant impact in scientific discovery, this is the perfect opportunity for you.

Benefits

Access to advanced technology

Innovative work environment

Collaborative team culture

Diversity and inclusion initiatives

Qualifications

• Principal-level expertise in Python and automation programming.
• Proven track record leading large-scale automation deployments.

Responsibilities

• Lead the design and deployment of innovative automation systems.
• Develop automation solutions for life science and material science applications.

Skills

Python programming

Automation engineering

Laboratory automation

System architecture

Project management (JIRA)

IoT systems

Hardware/software integration

Cross-functional collaboration

Education

Bachelor's degree in Biology, Chemistry, Engineering, or Material Science

Advanced degree in related fields

Tools

JIRA

PLC systems

SCADA technologies

Job description

Principal Automation Engineer, Workcell Builds

Cambridge, MA USA

Company Summary

Flagship Labs 97 Inc. (FL97) is a privately held, early-stage technology company pioneering the application of artificial intelligence to transform every aspect of the scientific method. FL97 is backed by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. Join our mission-driven team and contribute to the future of science.

Our Life Sciences effort is leveraging AI and high-throughput automation for valuable therapeutic discovery and development across biological modalities.

At FL97, we are uniquely cross-functional and collaborative. We are actively reimagining the way teams work together and communicate. Therefore, we seek individuals with an inclusive mindset and a diversity of thought. Our teams thrive in unstructured and creative environments. All voices are heard because we know that experience comes in many forms, skills are transferable, and passion goes a long way.

If this sounds like an environment you’d love to work in, even if you only have some of the experience listed below, please apply.

The Role

FL97 is seeking a dynamic and experienced Team Lead and Principal Automation Engineer to lead the design and deployment of innovative automation systems that bridge life sciences, material sciences, and industrial automation. This role focuses on creating scalable, integrated solutions by combining advanced laboratory automation with custom-engineered systems. Your leadership will drive cutting-edge automation in life science laboratories while expanding into material and physical sciences, supporting a wide range of applications including drug discovery, bioengineering, and advanced material characterization.

Responsibilities Include:

Life Science Lab Automation:

• Provide technical leadership in life science laboratory automation, architecting custom workcells.
• Design and oversee the development of integrated automation solutions for life sciences, leveraging off-the-shelf liquid handlers, sealers, peelers, schedulers, and other automation components, combined with custom-engineered hardware to meet specialized research needs.
• Implement advanced error recovery protocols and robust integration strategies for seamless operation of instruments like liquid handlers, analyzers, and robotic systems.

Material and Physical Science Applications:

• Develop automation solutions for material science research, including high-precision robotics for handling delicate materials and advanced control systems for experimental setups.
• Lead cross-functional collaborations to integrate physical science instruments with custom peripherals for automated workflows.
• Drive innovation in custom hardware development for physical sciences, enabling high-throughput experimentation.

System Design & Development:

• Architect and oversee the development of sophisticated automated systems that integrate commercial platforms, custom-engineered components, PLCs, and SCADA technologies to create hybrid laboratory and industrial automation environments.
• Design dynamic workflows using advanced Python programming and integrate with leading scheduling platforms such as Overlord, Cellario, and Green Button Go to optimize laboratory and material science operations.
• Guide the development of hardware and software standards for multi-vendor automation systems, ensuring compatibility across diverse scientific disciplines.
• Lead and mentor a team of automation engineers, fostering innovation and technical excellence.
• Promote collaboration between life science researchers, material scientists, and industrial engineers to create tailored automation solutions.

Strategic Planning:

• Develop long-term roadmaps for automation initiatives, emphasizing scalability and flexibility in life sciences and physical sciences environments.
• Lead technology selection for large-scale automation deployments, ensuring effective integration of custom hardware with commercial and analytical instruments.
• Drive continuous improvement in automation methodologies to enhance workflows in life science labs and material science research facilities.
• Implement IoT-enabled systems for real-time data monitoring and control in automated workflows for both biological and physical science applications.

Communication & Stakeholder Engagement:

• Represent technical leadership in stakeholder communications and vendor relationships, collaborating with partners to deliver customized solutions for advanced research.

Qualifications:

• Bachelor’s or advanced degree in Biology, Chemistry, Engineering, Material Science, or related fields. Certifications in automation or industrial engineering are advantageous.
• Principal-level expertise in Python and automation programming, including experience with modern automation frameworks and custom device integration.
• Proven track record leading large-scale automation deployments combining custom and commercial solutions.
• Deep experience with laboratory automation manufacturers and custom hardware integration.
• Demonstrated success managing teams of engineers to deliver innovative automation solutions in diverse scientific disciplines.
• Strong system architecture and strategic thinking capabilities for designing solutions that scale across laboratory and industrial environments.
• Expertise in dynamic workflow implementation and system optimization using real-time data from IoT-enabled devices.
• Knowledge of safety and compliance standards for automation in various research facilities.
• Experience with LIMS, ERP, and industrial data platforms.
• Proficient in using JIRA for project management and tracking agile development processes.
• Strong problem-solving skills for troubleshooting complex hardware/software integration challenges across disciplines.

Working at FL97, you would have access to advanced technology in the areas of:

• AI experimental design and simulation
• Automated custom instrumentation
• Generative molecular and material design

About Flagship

Flagship Pioneering is a platform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering and our ecosystem companies arecommitted to equal employment opportunityregardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.