# Senior Automation Engineer, Platform Biology

**Company**: Vesalius Therapeutics
**Location**: Cambridge, MA
**Experience**: senior
**Job type**: full-time
**Category**: Engineering
**Industry**: Healthcare

**Apply**: https://job-boards.greenhouse.io/flagshippioneeringinc/jobs/8651011002?utm_source=yubhub.co&utm_medium=jobs_feed&utm_campaign=apply
**Canonical**: https://yubhub.co/jobs/job_2efe0ab4-095

## Description

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?

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.

## Role Overview

As a Senior Automation Engineer, you will implement and scale the infrastructure behind our human cellular biology platform. You will work closely with cross-functional teams to design, develop, and deploy software solutions that enable scientists to efficiently conduct experiments and analyze data.

## Key Responsibilities

- Implement Benchling as a data platform, including entity schemas, Postgres warehouse, Insights, API, and supporting integrations.

- Establish sample tracking end-to-end, including chain of custody from donor material to instrument output.

- Deliver analysis-ready data to the data team, including structured metadata capture, stable identifiers, and documented schemas.

- Identify gaps in commercial software and design, ship, and operate REST APIs and internal web applications.

- Build integrations between automation platforms, instruments, LIMS/ELN, imaging systems, databases, and downstream data pipelines.

- Develop tools for scientists to use independently, such as search interfaces, pull lists, and capacity dashboards.

- Investigate and resolve discrepancies, and build checks to catch issues earlier.

- Apply sound software engineering practices, including version control, testing, debugging, and modular design.

- Partner across scientific, automation, IT, and data teams to bridge experimental work and recording systems.

- Anticipate future data and integration needs, plan for them, and stay flexible to learn 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.

- 4+ years of experience building software, tooling, or data infrastructure in a laboratory or R&D setting.

- Strong Python and SQL skills, including joins, aggregates, CTEs, and window functions.

- Deep hands-on experience with a LIMS or ELN and its API, preferably Benchling.

- Experience shipping and operating web applications, including REST APIs, front-ends, authentication, deployment, and maintenance.

- Experience with laboratory data flow, including sample registration, experiment execution, instrument output capture, and result attachment.

- Comfort with owning a domain independently, alongside strong scientific and hardware support.

- Strong communication and documentation skills, and ability to work effectively across teams.

## Preferred Experience

- Experience with Benchling, including entity schemas, warehouse, Insights, developer platform, webhooks, or apps.

- Parsing instrument output into structured results tied to samples.

- Cloud infrastructure, event-driven integrations, or data pipelines supporting automated laboratory environments.

- Working with automated liquid handlers, integrated workcells, or laboratory scheduling software.

- Mammalian cell culture at the bench, especially iPSC systems, and aseptic technique.

- Prior experience in an automation-heavy laboratory environment.

- Troubleshooting across software, hardware, instrument communication, data, and sample-tracking workflows.

- Mentoring or growing a small team.

- Experience in a regulated or GxP-adjacent environment, or writing validation and verification documentation.

## Skills

### Required
- Python
- SQL
- Benchling
- LIMS
- ELN
- REST APIs
- web development
- software engineering

### Nice to have
- AWS
- event-driven integrations
- data pipelines
- automated liquid handlers
- laboratory scheduling software
- mammalian cell culture
- iPSC systems
- aseptic technique

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