How Flock Bio's Scientists and AI Agents Work in the Same Loop
Flock Bio's scientists and AI agents run NGS pipelines, keep their notebooks and answer client questions in Cypher AI, and every run stays on one record the whole team can use.
CAMBRIDGE, MA · November 12, 2026
We're excited to share our new case study with Flock Bio, highlighting how they use Cypher AI!
Flock builds pooled DNA libraries for CRISPR screens, enzyme evolution and massively parallel reporter assays (MPRAs), and is also on the Cypher AI Marketplace. Its founders have spent more than 50 years between them making DNA and RNA libraries, at Affymetrix, Invitae, Twist, Circularis, Roche and Ginkgo. Flock has been working in Cypher AI since October 2025, and Matthew Youngblut, its co-founder and CSO, calls it "the platform I've wanted my entire career."
Scientists and AI agents working together
Matthew connected Flock's NGS pipelines to Cypher AI through our API, with each one versioned in GitHub. An AI agent, Claude Science in Flock's case, picks the pipeline, data and parameters, Cypher AI runs it in the cloud, and the agent reads the results and edits the pipeline for the next round. The scientists make the final calls.
A stable, shared system of record
Moving that fast only helps if the work is still there later. When AI runs iterations from one person's terminal, the rest of the team can't see what ran. In Cypher AI, every run is recorded the same way whether a scientist or an agent launched it, down to the exact pipeline version, so anyone on the team can trace a result back to its run, or rerun it months later.
"I only do NGS pipeline work on Cypher now. I need the durability and traceability."
— Matthew Youngblut, Co-founder and CSO, Flock Bio
The whole team, and Flock's clients
Not everyone at Flock works through code. The rest of the team launches pre-configured pipelines from the interface, asks the Cypher AI agent about past runs and files, and keeps its notes in Cypher's electronic lab notebook (ELN). Each client's work stays in its own project, and large sequencing files go out through secure download links.
Flock's clients see the benefit too. Every library is sequenced before it ships and comes with a QC report, and if a client asks, Flock can show them the pipeline run behind that report. Matthew says this gives customers "a level of visibility and reproducibility we simply couldn't achieve before."
A small team accomplishing a lot
As of October, Flock has more than 1,000 pipeline runs and 13 TB of pipeline data on record in Cypher AI, and the team once built seven tools on our API in a single day.
"The combined 8 of us between Flock and Cypher are doing things a 250-person company in 2023 couldn't do."
— Matthew Youngblut, Co-founder and CSO, Flock Bio
About Cypher
Cypher AI is building the intelligent digital infrastructure for life sciences R&D. Its AI-native platform unifies experiment design, execution, data management, and analysis into a single system, replacing fragmented tools with a cohesive, adaptive environment for modern research teams. By combining structured data with intelligent workflows, Cypher AI enables scientists to move faster from hypothesis to insight, improve reproducibility, and scale research without added operational complexity. The company works with biotech, pharma, and research organizations to accelerate discovery and innovation across the life sciences.