Engineer, Software Engineering

EngRadar; Cambridge (MA); On-site; USD 74,000 - 127,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering is seeking an Engineer, Software Development in Cambridge, MA to help design and evolve a biological research platform that turns experimental work into organized, analysis-ready data.

You will build data models, pipelines, and APIs, working with experimental scientists to ensure provenance and reproducibility, with cloud infrastructure and AI-enabled interfaces.

Qualifications

• 3+ years post-M.S. in CS or related field; biology exposure preferred.
• Hands-on programming and orchestration of AI coding agents.
• Data modelling with relational models, ORMs, and query implications.
• Experience with Python data engineering and cloud services (AWS).

Responsibilities

• Design reusable data models and workflows from experiments through implementation.
• Build pipelines to parse diverse files, harmonize metadata, and validate results.
• Create interfaces and APIs for data access and visualization.
• Configure secure cloud infrastructure and manage provenance and QC.
• Collaborate with experimental scientists to fit lab workflows into software.

Skills

Python

Data modelling

AI orchestration

AWS

REST APIs

Education

MS in Computer Science

Tools

PostgreSQL

SQLAlchemy

Alembic

FastAPI

Benchling

REST

MCP

Job description

Flagshippioneeringinc – Pioneering Medicines, an initiative of Flagship Pioneering, builds a biopharmaceutical R&D capability to develop life-changing treatments by harnessing Flagship's scientific platforms.

Cambridge, MA USA

What if you could help build a research platform that turns experimental biology into organized, accessible, analysis-ready data?

Experimental work generates data across many files, records, and systems, and manual handling of samples and results slows progress. A reliable computational platform can preserve sample lineage and experimental context and make data available through APIs, visualizations, and AI-enabled interfaces, so scientists can easily find, compare, and act on in-house data alongside the literature and other advances in the field.

FL103 is seeking an Engineer, Software Development to help design and evolve our biological research platform. The successful candidate will work with the computational modeling and experimental teams to learn how computational outputs become experimental inputs, how results return, and where manual handling slows progress. They will then move as much of that handling as practical onto reliable computational workflows that are transparent and easy to query.

FL103 was founded by Flagship Pioneering, an innovation enterprise dedicated to originating and developing companies that invent breakthrough technologies to transform health care, agriculture, and sustainability. Since Flagship’s founding in 2000, the firm has originated and fostered more than 100 scientific ventures, including Moderna Therapeutics, Generate Biomedicines, and Indigo Agriculture.

Position Summary

The successful candidate will help design and evolve a biological research platform that turns experimental work into organized, accessible, analysis-ready data. This is a platform and automation role, not a series of isolated programming tasks: the work is owned from design through operation, and the result should preserve sample lineage and experimental context.

Responsibilities

• Learn how experiments are run and how samples and results are tracked, and identify where manual handling slows progress.
• Identify recurring needs, design reusable data models and workflows, and carry them through implementation, testing, and operation.
• Design schemas and interfaces spanning computational screening inputs and outputs through final experimental records, connecting compute and experimental work and enabling powerful querying.
• Build or orchestrate pipelines that parse heterogeneous files and records, harmonize metadata, validate results, and load shared systems, replacing repetitive manual steps with recoverable workflows across laboratory records, cloud storage, databases, and external services.
• Make data available through APIs, visualizations, and AI-enabled interfaces.
• Configure and operate shared cloud infrastructure safely, distinguishing between testing a change and applying it.
• Preserve provenance, units, controls, and QC; write meaningful tests; and catch bad joins or transformations, including in generated code.
• Work directly with experimental scientists on metadata conventions, ambiguous records, and workflows that fit how the lab works, so the team can easily find, compare, and act on in-house data alongside the literature and other advances in the field.

Qualifications

• 3+ Years of experience post M.S., preferably in Computer Science, exposure to biology preferable
• Hands-on programming, effective orchestration of AI coding agents, or both, with the ability to specify architecture and constraints, validate what is built, and take responsibility for the result
• Data modelling skills, including relational models and ORMs, sample and experiment identity, and how modelling choices affect later queries (current stack: PostgreSQL on AWS RDS, SQLAlchemy, and Alembic)
• Python data engineering experience (Pandas, NumPy, and PyArrow are useful)
• Integration and automation experience (current stack: FastAPI, Benchling, REST, and MCP)
• Working knowledge of AWS (S3, RDS, EC2, Secrets Manager, and Bedrock), including credentials and permissions
• Strong judgement on data integrity. Demonstrated delivery matters more than any particular tool, or than having written every component by hand
• Biological knowledge strongly preferred (genes and proteins, cell types, antibody assays, transcriptomics, proteomics, controls, and replicates), and comfort collaborating with experimental scientists

Helpful, But Not Required

• Laboratory automation: connecting instruments or control systems to software and AWS. The role may later extend from data handling into experimental automation.
• LLM applications: structured extraction, evidence checks, evaluation, and cost control with Bedrock, Anthropic, or OpenAI.
• Interfaces: React/TypeScript, Vite, and Plotly.
• Familiarity with relational databases

The salary range for this role is $74,000 - $126,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience.

FL103 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.

Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.