Post-Setup

Once bioAF is running and you’ve pasted the one-time setup code from ./bioaf setup into the web UI to create your admin account, there are a few things to set up before your team starts using the platform.

Enable platform components

By default, bioAF starts with the core platform only. Additional capabilities are enabled through the Component Settings page.

  1. Navigate to Admin > Component Settings
  2. Review the available components and their estimated monthly costs
  3. Toggle on the ones your team needs
  4. Review the infrastructure plan that bioAF generates
  5. Confirm to provision

Component Settings page showing available components with cost estimates and toggle switches

i What's happening when I toggle a component?
When you enable a component, bioAF generates a Terraform plan, a description of the cloud resources it needs to create. You review the plan (including cost estimates) and confirm. bioAF then provisions those resources in your GCP project. You can disable components later to remove the resources and stop incurring costs.

For a typical scRNA-seq team:

  • GKE cluster: Required for running pipelines and notebooks
  • Cloud SQL: Required for the database (usually provisioned during setup)
  • GCS buckets: Required for data storage
  • JupyterHub or RStudio: For interactive analysis
  • cellxgene: For single-cell visualization

Invite your team

  1. Navigate to Admin > Users
  2. Click Add User
  3. Enter their email and assign a role

Built-in roles

Role Can do
Admin Everything, manage users, roles, components, and platform settings
Computational Biologist Run pipelines, launch notebooks, manage environments, upload/download data
Scientist Register experiments, add samples, upload data, view results
Viewer Browse experiments, view results, download files (read-only)

You can also create custom roles with fine-grained permissions under Admin > Roles.

Configure notifications

bioAF can send notifications when pipelines complete, QC results are ready, or budget thresholds are hit.

  • In-app notifications: Enabled by default
  • Email: Configure SMTP settings under Admin > SMTP Settings
  • Slack: Add a webhook URL under Admin > Slack Settings

Next steps

Your platform is ready. Point your team to the guide for their role: