Quick Start

Use this walkthrough to load one study and ask the first question.

Before You Start

You need:

  • the project installed; see Installation;

  • one study folder under data/raw/{STUDY_NAME}/;

  • a local Ollama model or a hosted LLM API key;

  • access to the web UI. The web UI creates the local PHI key during study load when needed.

1. Place Study Files

Expected layout:

data/raw/Indo-VAP/
├── datasets/
├── data_dictionary/
└── annotated_pdfs/        # optional

Set the study name if needed:

export STUDY_NAME=Indo-VAP

On Windows PowerShell, use $env:STUDY_NAME = "Indo-VAP" instead.

2. Choose a Model Provider

Recommended local setup:

export LLM_PROVIDER=ollama
export LLM_MODEL=qwen3:8b

Hosted provider example:

export LLM_PROVIDER=anthropic
export ANTHROPIC_API_KEY=sk-ant-...
export LLM_MODEL=claude-opus-4-7

On Windows PowerShell, set environment variables with $env:NAME = "value". You can also choose the provider from the web UI instead of setting these values in the shell.

See Configuration for OpenAI, Google, and PDF-related settings.

3. Load the Study

Use the web UI:

make chat

Then click Load Study.

The command-line make pipeline path is for developers and deployment operators who have already provisioned the local PHI key.

Expected result:

output/Indo-VAP/
├── trio_bundle/
├── audit/
└── agent/

4. Start Chat

If the web UI is not already open:

make chat

Ask a simple first question, for example:

How many subjects are in this study?

Then try a study-specific question:

What variables are available for baseline demographics?

Use Existing Study

If the study team has saved a reviewed snapshot, choose Use Existing Study. The portal restores data/snapshots/{STUDY}/ into output/{STUDY}/trio_bundle/ before chat.

Common Problems

PHI key not found

Use Load Study in the web UI. It creates the local PHI key when needed. If the command-line pipeline reports this error, ask a developer or operator to provision the key.

Study not found

Confirm STUDY_NAME matches the folder under data/raw/.

API key not found

Export the key for the selected hosted provider, or use Ollama.

PDF warning

PDFs are optional. If PDFs may contain PHI, review Configuration before enabling hosted PDF processing.

Next Steps