Quick start

Use this guide to run your first Immunology workflow.

1. Open Immunology

Go to Research Areas -> Immunology or visit:

/areas/immunology/dashboard

The dashboard lists recent studies and provides a create-study action.

2. Create a study

Create a study with:

Field	Example
Name	SLE PBMC cohort
Disease context	autoimmune
Organism	human
Cohort label	baseline vs treated

After creation, the study detail page becomes the main workspace.

3. Register datasets

Use dataset records to track modality and file metadata. Supported modalities include:

• scrna
• cite_seq
• vdj
• spatial
• bulk_rna
• atac
• fcs
• cytokine

The current UI records dataset metadata. Analysis panels can also run with demo/tabular inputs when no file path is provided.

4. Run a first analysis

Start with Immune composition. It summarizes immune population counts and proportions from cell annotation rows.

Then add deeper analyses:

• Annotation and state scoring for hierarchy labels and immune state scores
• TCR/BCR repertoire for clonotypes and diversity
• Cell-cell communication for ligand-receptor and cytokine signaling
• Disease workflows for trajectory, spatial, and cohort summaries
• Multi-modal profiling for ADT, ATAC, and cytometry-like event tables

5. Interpret and report

Once at least one completed analysis run exists, use AI interpretation and reporting to generate:

• grounded interpretation with metric citations
• methods text
• report templates
• figure export specs
• provenance snapshots

Interpretation uses the configured Ollama gpt-oss:120b model when available and a deterministic fallback when the LLM service is unavailable.