Scientific Software Engineer

Department: Software

Location: Amsterdam

Employment Type: FullTime

This is Cradle

Proteins are the molecular machines of life, used for many therapeutic, diagnostic, chemical, agricultural and food applications. Designing and optimizing proteins takes a lot of expert knowledge and manual effort, through the use of custom computational and biological tools.

Machine learning is revolutionizing this space, by enabling high-fidelity protein models. At Cradle, we offer a software platform for AI-guided discovery and optimization of proteins, so that biologists can design proteins faster and at scale. We are already used by clients across biopharma, biotech, agri-tech, food-tech, and academia.

We're an experienced team of around 75 people. We've built many successful products before and have enough funding for multiple years of runway. We are distributed across two main locations, Zurich and Amsterdam, and are focused on building the best possible team culture.

We offer our employees a very competitive salary, a generous equity stake in the company and a wide range of benefits and career progression opportunities.

What we're building

Cradle is building the future of protein engineering. Our AI platform helps scientists design better proteins faster, with customers including Novo Nordisk, Johnson & Johnson, and Grifols. We've raised over $100M to bring ML-powered protein engineering to labs worldwide.

Our in-house wet lab in Amsterdam serves a unique purpose: we generate the high-quality data our ML models need to learn, build showcases that demonstrate what's possible, and develop best practices we share openly with the field. We believe the future of biotech depends on "ML-ready" labs, and we're building the playbook by sharing scripts, protocols, and practices that help our customers (and future customers) generate the data our platform needs.

The Role

We're looking for a software engineer to build the critical software infrastructure that connects systems across our lab ecosystem. You'll bridge lab equipment, data systems, and scientists, building the glue that makes our lab easier to work in.

This role formally sits within Software Engineering but is 100% dedicated to supporting BioEngineering. You'll pair with scientists and bioinformatics experts to understand problems, then build software solutions.

What You'll Do

To give you a flavour of the projects you'd work on:

Connect lab equipment and tools
Build bidirectional connections between our lab instruments and Benchling using UniteLabs' integration platform and Python SDK. This means pulling data from machines (plate readers, sequencers, NanoDSF, LabChip, Carterra) into our data warehouse, and controlling instruments programmatically. Build reliable ETL pipelines that capture experimental results.

Develop in silico analysis workflows
Write the scientific analysis logic that turns raw experimental data into results. This includes NGS analysis pipelines for Illumina and Nanopore data (if these terms are not familiar to you, don’t fret: you'll pair with a bioinformatician), and algorithms for interpreting characterization assays. A concrete example: analyzing photos from our colony picker to detect colonies using object recognition, then triggering the picker to pick them.

Build and maintain workflows
Develop and refactor in silico (Flyte) workflows that orchestrate laboratory processes. Create robust, testable systems that handle the complexity of real lab operations.

Lab automation workcell
Build a user-friendly interface for our robotic workcell (a robotic arm coordinating multiple instruments). The goal is a low-barrier, walk-up system where running an experiment is easy. This includes frontend, backend, and the connection layer to our existing machine drivers.

Contribute to open-source initiatives
Help us share tools, SDKs, and workflows with the broader scientific community. You'll work on building integrations and tools that make it easier for other organizations to adopt Cradle and connect it with their lab ecosystems, lowering barriers to entry for protein engineering teams worldwide.

What You Bring

Technical foundation

• 2+ years of industrial software development experience

• Strong Python development and API integration experience

• Comfort with SQL databases and data engineering concepts

• Frontend development skills for building lab dashboards and interface

Builder mentality

• You love rolling up your sleeves and building things from the ground up

• You're comfortable working at the intersection of software and hardware

• You can communicate effectively with both software engineers and domain experts

• You're excited about learning new domains and tackling diverse technical challenges

Not required

• A PhD

• Prior biotech or domain experience

Learning More About the BioEngineering Team

We're quite open about what we work on. If you'd like to learn more before applying, check out blog posts from our team (link 1, link 2) or watch the webinar we did with Lab Services on how we’re using automation in our lab (link).

Our commitment to inclusive hiring

Cradle evaluates all candidates based on merit, regardless of sex, gender, ethnicity, socio-economic background, or any other aspect of identity. We maintain zero tolerance for discrimination and actively encourage candidates from all backgrounds to apply.

AI disclosure

Cradle uses an applicant tracking system that includes basic AI-assisted features which may generate scores or rankings based on how applications match a job description. These outputs are not used to make or meaningfully influence hiring decisions — all candidates are evaluated through a thorough, human-led review by our recruiting team.

A notice about recruitment scams

Please be aware that scammers are posing as us in order to get your personal details or money. We only communicate via @cradle.bio email addresses, we only make job offers after having met you in person at our office in Zurich or Amsterdam, and we never ask you to pay for anything during the interview process.