Senior Automation Engineer for Scalable Biotech Workcells

Flagship Pioneering, Inc.

Cambridge (MA)

On-site

USD 108,000 - 171,000

Full time

14 days+

A complete application in a minute

Tailored resume and cover letter, ready to send.

Get past ATS filters

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Other benefits

Job summary

Vesalius Therapeutics in Cambridge, MA is seeking an Automation Engineer to scale our automated biology platform. You will translate workflows into robust workcells, integrate instruments, and partner with scientists, automation operators, IT, and data science.

This early-career role focuses on programming, data handling, and software engineering practices to deliver reliable, traceable data and scalable automation solutions across platforms such as Hamilton STAR and similar systems.

Qualifications

Bachelor’s or master's degree in computer science, engineering, bioengineering, automation, robotics, biomedical engineering, computational biology, or related field.
Early career experience in laboratory automation, scientific software, robotics, biotech automation, or a related environment.
Experience with biological workflows such as mammalian cell culture, cell-based assays, high-content imaging, high-throughput screening, NGS, or iPSC systems is strongly preferred.
Hands-on experience with automated liquid handlers, robotic systems, integrated workcells, laboratory scheduling software, or instrument-control methods.
Experience developing and troubleshooting automated biological workflows, liquid-handling methods, instrument workflows, software tools, or systems integrations.

Responsibilities

Develop and optimize high-throughput automated protocols that translate biological workflows from the bench to integrated workcells.
Partner with scientific teams to design automation solutions that balance biological fidelity, throughput, cost, reliability, and lead time.
Collaborate with scientists and automation operators on workflow execution, troubleshooting, training, and continuous improvement.
Develop and maintain automation scripts, scheduling workflows, error handling, monitoring, and instrument-control methods using tools such as Python, C#, JSON, platform APIs, and vendor-specific languages.
Validate automated workflows against benchtop methods, assessing precision, accuracy, reproducibility, and data quality.
Build integrations between automation platforms, instruments, LIMS/ELN, imaging systems, databases, and downstream data pipelines, including structured metadata capture and data handoff.
Integrate and troubleshoot new instruments and workcell components, including instrument interfaces or drivers where needed.
Apply sound software engineering practices including version control, testing, debugging, modular design, and documentation.
Program liquid-handling and robotic workflows across platforms such as Hamilton STAR, Dynamic Devices Lynx, HighRes Biosolutions/Cellario, and similar systems.
Develop barcode to workflow mapping to enable batch and sample tracking.
Create and maintain SOPs, method documentation, validation reports, troubleshooting guides, and other technical documentation.