Senior Automation Engineer - Platform Biology

What if you could join a rapidly growing company and play a critical role in bringing new medicines to patients by helping scale the programmable infrastructure behind a new human cellular biology platform?

About Vesalius

Vesalius Therapeutics is pioneering a new platform to generate breakthrough treatments for common diseases. Our platform combines large-scale human genetics, genomics, stem cell studies, high-dimensional cellular phenotyping, and artificial intelligence to uncover causal biology and identify optimal intervention points for new therapies. Vesalius was founded in 2019 by Flagship Pioneering.

Role Overview

Vesalius is seeking a highly motivated Automation Engineer to help scale our automated biology platform. This early-career role sits at the intersection of biology, robotics, software, and data systems, with a focus on programming, data handling, systems integration, and workflow automation.

You will partner with scientists, automation operators, IT, and data science teams to translate biological workflows into robust automated workcells and ensure experiments generate reliable, traceable, analysis-ready data. This role goes beyond operating instruments—it is focused on making automation programmable, integrated, scalable, and reliable.

Key Responsibilities

• Implement Benchling as a data platform, not only as an ELN: entity schemas, the Postgres warehouse, Insights, the API, and the supporting integrations.
• Establish sample tracking end to end. Chain of custody from donor material through line, vial, thaw, run and instrument output, and the links that let a result be attached back to the sample that produced it.
• Deliver analysis-ready data to the data team, including structured metadata capture, stable identifiers, and documented schemas with reliable handoff.
• Identify gaps in commercial software and design, ship and operate REST APIs and internal web applications, for example a results parser, a scheduling interface, or an app to integrate Benchling.
• Build integrations between automation platforms, instruments, LIMS/ELN, imaging systems, databases and downstream data pipelines.
• Build tools scientists use independently: search interfaces, pull lists, capacity dashboards.
• Investigate and resolve discrepancies, such as inventory that does not reconcile after a migration, and build the checks that catch them earlier.
• Apply sound software engineering practice: version control, testing, debugging, modular design, and documentation that someone else can maintain.
• Partner across scientific, automation, IT and data teams, bridging experimental work and the systems that record it.
• Anticipate future data and integration needs, plan for them, and stay flexible about learning new systems as the platform evolves.

Qualifications

• Bachelor's or master's degree in computer science, engineering, bioengineering, biomedical engineering, computational biology or a related field, or a life science degree with a demonstrated programming record.
• 4+ years building software, tooling or data infrastructure in a laboratory or R&D setting, including time as the person accountable for a system other people depended on daily.
• Strong Python and SQL: joins, aggregates, CTEs and window functions.
• Deep hands-on experience with a LIMS or ELN and its API. Benchling strongly preferred; Sapio, Dotmatics, LabVantage or similar all count.
• Experience shipping and operating a web application: a REST API, a front-end for other users, including authentication, deployment and maintenance.
• Experience with how data moves through a laboratory: how a sample is registered, how it becomes an experiment, how instrument output is captured, and how a result is attached back to the sample.
• Comfort with owning a domain independently, alongside strong scientific and hardware support.
• Strong communication and documentation skills, and the ability to work effectively across scientific, automation, IT and data teams.

Preferred Experience

• Benchling: entity schemas, the warehouse, Insights, the developer platform, webhooks or apps.
• Parsing instrument output (plate readers, imagers, sequencers) into structured results tied to a sample.
• Cloud infrastructure such as AWS, event-driven integrations, or data pipelines supporting automated laboratory environments.
• Working alongside automated liquid handlers, integrated workcells or laboratory scheduling software (Hamilton, Tecan, HighRes Biosolutions, Dynamic Devices, Beckman or similar), as an integrator rather than a programmer.
• Mammalian cell culture at the bench, especially iPSC systems, and aseptic technique.
• Prior experience working in an automation-heavy laboratory environment.
• Ability to troubleshoot across software, hardware, instrument communication, data and sample-tracking workflows.
• Mentoring, or growing a small team.
• A regulated or GxP-adjacent environment or writing validation and verification documentation.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $108,000 - $170,700. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Vesalius Therapeutics currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Vesalius Therapeutics's good faith estimate as of the date of publication and may be modified in the future.

Pay Range: 108000.0 - 170700.0 USD