Case study · Flock Bio
One platform where scientists and AI agents work in the same loop
At Flock Bio, scientists and AI agents run NGS pipelines, ask the Cypher AI agent about past runs and keep their notebooks in the Cypher ELN. The team can trace, review and rerun the work from one shared record.
“I only do NGS pipeline work on Cypher now. I need the durability and traceability.”
Matthew YoungblutCo-founder and CSO, Flock Bio
Download the case study
Two pages: how Flock runs its Nextflow pipelines through Cypher AI, and what each run keeps on the record.
- Pipeline runs on record
- 1,000+
- Tools built on the API in one day
- 7
- Pipeline data stored
- 13+ TB
- Customer since
- Oct 2025
Figures as of October 2026.
Inside the case study
One record for scientists, agents and the whole team.
Flock Bio builds pooled DNA libraries for CRISPR screens, enzyme evolution and MPRAs. When AI runs the iterations from one person’s terminal, colleagues can’t review earlier runs, reproduce results or share outputs with clients.
Pipelines through the APIFlock’s Nextflow pipelines are versioned in GitHub. An AI agent, Claude Science at Flock, picks the pipeline, data and parameters; Cypher AI runs it in the cloud and records the version used.
Every run on the recordWhether a scientist or an agent launched it: the exact commit, container and parameters, the files and logs, and the compute it used.
Pipelines for the whole teamColleagues who don’t work in code launch pre-configured pipelines from the interface and ask the Cypher AI agent about past runs and files.
Electronic lab notebookThe team keeps its notes in the Cypher ELN, in the same system as its pipelines and data.
QC reports with their runsEvery library ships with a QC report, and the run behind it stays on the record for the team and for the client who asks.
Client projects, kept secureEach client’s work stays in its own project, and large deliverables go out through secure download links. Flock’s own single-tenant instance in its AWS account, SOC 2 Type II, with Claude on Amazon Bedrock and zero data retention.
“The combined 8 of us between Flock and Cypher are doing things a 250-person company in 2023 couldn’t do.”
Matthew YoungblutCo-founder and CSO, Flock Bio