Reusable prompts for precision medicine analyses. Copy, paste, and customize for your use case.
| Audience | File | Prompts | Time Range |
|---|---|---|---|
| Funders & Decision-Makers | funder-demo.md | 7 prompts | 5-10 min each |
| Clinicians & Researchers | clinical-workflow.md | 15 prompts | 5-45 min each |
| Developers & QA | developer-testing.md | 11 prompts | 1-15 min each |
| Students & Educators | educational.md | 10 prompts | 5-20 min each |
| Modality | File | Prompts | Servers |
|---|---|---|---|
| Clinical & Genomic | clinical-genomic.md | 17 | mcp-mockepic, mcp-fgbio, mcp-genomic-results |
| Multi-Omics | multiomics.md | 17 | mcp-multiomics |
| Spatial Transcriptomics | spatial.md | 18 | mcp-spatialtools |
| Imaging | imaging.md | 8 | mcp-deepcell, mcp-cell-classify, mcp-openimagedata |
| External Data & Drug Targets | — | — | mcp-geodownload, mcp-opentargets |
| Immunology & Neoantigen | — | — | mcp-cibersortx, mcp-neoantigen |
| End-to-End Workflows | workflows.md | 10 | All servers (see Registry) |
Full profile: PatientOne Profile | Cost details: Cost Analysis
- Patient ID:
PAT001-OVC-2025 - Diagnosis: Stage IV HGSOC, platinum-resistant, BRCA1 germline mutation
- Key mutations: TP53 R175H (73% VAF), PIK3CA E545K (42%), PTEN LOH (85%)
- GCS data:
gs://sample-inputs-patientone/patient-data/PAT001-OVC-2025/ - Local data:
data/patient-data/PAT001-OVC-2025/
Write prompts that are specific, include parameters, and specify expected output:
# Too vague
Analyze PatientOne data
# Better — specific, parameterized, output-directed
Perform spatial pathway enrichment on PatientOne (PAT001-OVC-2025) tumor regions.
Spatial data is in GCS at gs://sample-inputs-patientone/patient-data/PAT001-OVC-2025/spatial/.
Focus on cancer-related KEGG pathways with FDR < 0.05.
Return top 10 enriched pathways with p-values and gene counts.
For multi-step analyses, number each step and name the MCP server to use.
- PatientOne Guide - Complete walkthrough
- Test Prompts - 10 DRY_RUN + 4 SYNTHETIC_DATA test scenarios (canonical source for PatientOne Prompts 1-6)
- Immunotherapy Reference - Cold tumor candidates
- Server Documentation - Tool reference
- Connect External MCP Servers - ClinicalTrials.gov, PubMed, bioRxiv, Hugging Face, cBioPortal, Seqera
Last Updated: 2026-03-09