Role & seniority: Automation Engineer (mid-level) focused on automating in-house manufacturing and research protocols; contribute to platform strategy and open-source ecosystem.

Stack/tools: Opentrons-based automation stack; lab equipment (Plate Readers, LabChip); Python (architecture, API design, testing, docs); lab data management; potential exposure to NextFlow/SnakeMake/APache Airflow; familiarity with LIMS and data analytics.

Top 3 responsibilities

Convert manual processes into high-throughput, automated workflows; design, run, and analyze experiments to validate automation.
Maintain and extend internal automation codebase (Opentrons and related systems); onboard and support lab automation equipment.
Document workflows, train teams, provide ongoing technical support; implement QC/standards for reproducibility; contribute to long-term platform strategy.

Must-have skills

2+ years in lab automation, preferably with Opentrons, Hamilton, or Tecan.
Practical wet-lab molecular biology experience; strong Python development (architecture, API design, version control, testing).
Experience with data management, metadata standards, and QC/analytical feedback loops; strong communication and collaboration.

Nice-to-haves

Custom hardware integrations, robotic peripherals, biomanufacturing or synthetic biology experience.
Experience with computational analysis tools (Jupyter, similar), workflow orchestration (NextFlow, Snakemake, Airflow).

Full Description

Overview We’re looking for an Automation Engineer who will take ownership of automating our in-house manufacturing and research protocols, evolve these systems into robust production-grade infrastructure, and deploy them to our manufacturing and research teams.

You will collaborate closely with our team of biologists, engineers, and biomanufacturers, beginning by building on our existing automation stack (Opentrons) to automate critical processes and high-throughput Compositional Biology experiments. Your work will contribute directly to our open-source synthetic cell platform, advancing both our internal capabilities and the broader open-source ecosystem driving compositional biology forward.

Geographic Considerations: Full-time in-person (San Francisco, CA)

Responsibilities Collaborate with biologists and engineers to convert manual processes into reliable, high-throughput, automated workflows. Build upon, extend, and maintain our internal codebase for automation (e.g Opentrons and related systems) Design, run, and analyze experiments to develop and validate automated processes. Translate automated processes to lab operations through documentation, training, and ongoing technical support. Design and implement metrics, standards, and QC to ensure liquid handling reproducibility and consistency. Operate and monitor automated processes for ongoing research and development projects. Onboard, operate, and support key lab and automation equipment. (e.g., Plate Readers, LabChip, etc.). Document automation workflows, interfaces, and best practices for team scalability. Contribute to long-term platform strategy—improving the pace and reliability of our bioengineering efforts.

Qualifications Demonstrated success automating biological or chemical processes. 2+ years experience in lab automation, preferably with Opentrons, Hamilton, or Tecan systems. Understanding of and practical experience with wet-lab molecular biology or related field. Strong Python development skills (e.g., architecture, API design, version control, documentation, unit and integration testing) Familiarity with lab data management (e.g., analytical data, plate maps, workflow orchestration, instrument logs, metadata standards). Experience implementing QC or analytical feedback loops in automated workflows. Strong written and oral communication, and collaboration practices. Detail-oriented, systematic thinker with an ability to bridge experimental workflows to code.

Bonus Expertise Experience with custom hardware integrations and robotic peripherals. Experience in biomanufacturing, protein production, synthetic biology. Experience with computational scientific analysis tools (e.g. Jupyter, Marimo). Experience with workflow automation tools (e.g., NextFlow, SnakeMake, Apache Airflow). Ability to connect lab automation to broader digital infrastructure (e.g., LIMS, scheduling, data analytics). Comfortable onboarding, maintaining, and troubleshooting diverse lab instruments.