Biotech Data Engineer: End-to-End Scientific Pipelines

Matterworks, Inc.; Somerville (MA); Hybrid; USD 120,000 - 180,000; Full time

Benefits offered by this job

Stock options

Health and dental

Vision coverage

Disability insurance

Life insurance

401k with match

Flexible time off

Commuter benefits

Team meals

Education support

Conference access

Job summary

Matterworks, Inc. is seeking a Data Engineer to build and run the pipelines behind our models. Our platform ingests mass spectrometry data at scale and turns it into datasets for AI training and product reasoning.

You will own pieces end to end and collaborate with ML researchers, scientists, and the product team. This hands-on role offers growth as you start with scoped pipelines and expand to larger platform areas, reporting to the Head of Engineering in a flexible hybrid setup from

Qualifications

• 2+ years of professional experience building data pipelines in production.
• Proficient in Python and SQL.
• Working knowledge of cloud data infrastructure. We run Argo Workflows and Metaflow on EKS, Glue and Athena over Apache Iceberg and Parquet, DuckDB, and Terraform. Depth in any comparable stack transfers fine.
• Demonstrated experience owning a pipeline or dataset end to end, including the tests, the monitoring, and the failures.
• Comfort with messy data and messy formats, and the patience to track down why two sources disagree.
• Daily use of AI coding tools, paired with healthy skepticism about their output on questions of production data correctness.
• Clear written communication, particularly when explaining what broke and what you changed.
• Curiosity about the science. Experience in life sciences, biotechnology, or biochemistry is a plus but not a requirement, and you will work alongside strong in-house chemistry every day.
• A passion for contributing to an early-stage startup where autonomy, eagerness to learn, and enthusiasm for solving novel scientific challenges prevail over rigid processes and egos.

Responsibilities

• Build and Operate Pipelines: Own well-scoped pipelines end to end: designed, tested, instrumented, documented, and running on a schedule.
• Labels and Enrichment: Turn raw data into datasets people can actually use, with consistent schemas, trustworthy metadata, and documented definitions.
• Data Quality Checks: Design, build and extend our quality checks so that each build gets compared against the last one before it publishes, and a failure stops the pipeline instead of shipping.
• Ingest and Acquisition: Bring new public and partner datasets into the platform: fetching, converting, validating, and reconciling them against what we already hold. Expect messy scientific and vendor formats and file that require continuous improvements to our systems to handle at scale.

Skills

Data pipelines

Python

SQL

Cloud infra

Argo Workflows

Metaflow

Terraform

Glue

Athena

Iceberg

Parquet

DuckDB

EKS

End-to-end ownership

Data quality checks

Tools

Argo Workflows

Metaflow

Terraform

AWS Glue

Amazon Athena

Apache Iceberg

Parquet

DuckDB

EKS

Job description

Matterworks, Inc. is seeking a Data Engineer to build and run the pipelines behind our models. Our platform ingests mass spectrometry data at scale and turns it into datasets for AI training and product reasoning.

You will own pieces end to end and collaborate with ML researchers, scientists, and the product team. This hands-on role offers growth as you start with scoped pipelines and expand to larger platform areas, reporting to the Head of Engineering in a flexible hybrid setup from