Computational biology infrastructure
in minutes, not months.
bioAF gives small biotech teams production-grade pipelines, notebooks, and experiment tracking on day one. No DevOps engineer required.
One command. One working platform.
What used to take a quarter of DevOps work runs in the time it takes to grab coffee. No compute team, no install guide, no babysitting.
bash <(curl -fsSL https://raw.githubusercontent.com/bioAF/bioAF/main/install-gcp.sh)
Choose public or private IP. Paste the one-time setup code into the URL it prints to claim your admin account.
- Provisions GCP: VM, firewall, and a service account scoped to your project.
- Builds the stack: containers, dependencies, and environment configuration.
- Runs migrations: PostgreSQL schema and seed data ready for the first sign-in.
- Brings up every service: web UI, API, workers, JupyterHub, RStudio, and the pipeline runner.
Powered by tools that stand on their own
bioAF is an orchestration layer, not a walled garden. It builds on industry standard tools you already know.
Industry-standard foundations
Everything bioAF provisions and manages (Kubernetes, PostgreSQL, Nextflow, JupyterHub, RStudio, GCS) is mature, widely-adopted, and has large communities behind it. bioAF didn't invent any of it. It just wires it together.
You own everything
Your data lives in your GCP project. Your infrastructure is defined in Terraform you can export at any time. There are no proprietary formats, no hosted dependencies, and no gates between you and your own work.
Replace bioAF at any time
If your needs change, or if this project stops being maintained, you can replace bioAF's control plane with your own tooling and everything underneath keeps working. The pipelines still run. The data is still there. The notebooks still launch.
Bioinformatics
Analysis & Compute
Infrastructure
Built for your whole team
Multi-user from day one. Customizable roles and access controls grow with your team from bench to boardroom.
Bioinformaticians
Run scRNA-seq pipelines, launch Jupyter or RStudio with versioned environments, and access your data, all from one place.
Bench Scientists
Register experiments, upload FASTQ files, and explore results with interactive visualizations. No command line needed.
PIs & Lab Managers
Track team progress, monitor cloud costs, and maintain a complete audit trail from sample to publication.
From zero to science in four steps
Deploy
Run one command on your laptop. It provisions GCP, builds the stack, brings up every service, and prints a URL with a one-time setup code so you can claim your admin account.
What happens under the hood?
./install-gcp.sh sets up the gcloud CLI, creates the VM, firewall rules, and service account, then builds the containers, runs migrations, starts the services, and prints a one-time setup code that proves you have admin access. You choose whether the VM uses a public or private IP.
Experiment
Create experiments with structured metadata and add your samples. bioAF tracks everything from bench to results.
Run
Launch pipelines from the built-in catalog or start a notebook session. Monitor progress in real time.
What pipelines are included?
Explore
View QC dashboards, browse results in cellxgene, and share findings with your team.
Everything you need, nothing you don't
A complete platform for computational biology at small biotech scale.
Pipeline Execution
Run Nextflow workflows from a built-in catalog, or author your own. Any program that runs on Linux, version-pinned and reproducible.
Notebook Sessions
Launch JupyterHub or RStudio with versioned environments and automatic idle shutdown.
Experiment Tracking
MINSEQE-compliant metadata, sample batches, and a full status lifecycle from registration to completion.
Interactive Visualization
Browse single-cell datasets in CellxGene Discover, review QC dashboards, and search the plot archive.
Cost Management
Components auto-scale to control cost when not in use. See per-project spend, set budget alerts, and track trends over time.
Audit & Compliance
An immutable audit trail with full provenance - who did what, when, and why.
Data Management
Upload, browse, and download files with automatic lifecycle management across storage tiers.
Infrastructure Management
Enable or disable platform components from the UI. See cost estimates before you provision anything.
Auto-Ingest
Connect to your CRO, cloud storage, or sequencer and let bioAF automatically detect and import new files as they arrive.
