BioRouter Workflows

Community workflows for BioRouter — an AI-powered integrated research environment for biomedical discovery built by UCSF's Baranzini Lab.

What are Workflows?

Workflows (.yaml files) define reusable AI agent tasks in BioRouter. Each workflow specifies:

• A title and description
• Instructions for the agent
• Activities (example prompts to get started)
• Extensions (built-in MCP tools the agent can use)

Available Workflows

Workflow	Description
EHR Diabetes Dashboard	Query an OMOP-based EHR for a T2D patient cohort, summarize demographics, and produce HTML reports or R Shiny dashboards

How to Use

1. Copy a .yaml file from the workflows/ directory.
2. Place it in your BioRouter workflows directory (~/.config/biorouter/skills/ or via the BioRouter UI).
3. Load the workflow in BioRouter and start with one of the suggested activities.

Contributing

Submit a pull request to share your own BioRouter workflows with the community!