How to: reproduce paper workflows

BioMCP paper-style workflows are best reproduced with direct CLI commands. If you want the agent-facing guide first, run biomcp skill or install it into your agent directory, then execute the commands that match the paper pattern you want to reproduce.

Mapping

Paper-style workflow	BioMCP workflow area	Representative commands
GeneGPT	gene, variant, trial, and article walkthroughs	biomcp get gene BRAF, biomcp get variant "BRAF V600E" population, biomcp variant trials "BRAF V600E" --limit 3, biomcp search article -g BRAF -d melanoma --limit 3
GeneAgent	pathway, drug, and protein synthesis	biomcp get pathway R-HSA-5673001 genes, biomcp pathway drugs R-HSA-5673001 --limit 3, biomcp protein structures P15056
TrialGPT	trial discovery and patient matching	biomcp search trial -c melanoma --mutation "BRAF V600E" --status recruiting --limit 5
PubMed & Beyond	literature synthesis	biomcp search article -g BRAF -d melanoma --limit 5, biomcp get article 22663011 fulltext

Suggested execution pattern

1. Pick the workflow area that matches the paper task.
2. Run the direct CLI commands for that area.
3. Save command output in a markdown log with stable IDs such as PMIDs, gene symbols, pathway IDs, and NCT IDs.
4. Verify the final summary against the paper's reported entities and evidence.

Example session

biomcp get gene BRAF
biomcp get variant "BRAF V600E" population
biomcp search trial -c melanoma --mutation "BRAF V600E" --status recruiting --limit 5
biomcp get article 22663011 fulltext

Notes

• The BioMCP guide is optional context, not the primary execution path.
• If a service is temporarily rate limited, retry after a short pause.
• If enrichment is unavailable, continue with pathway, interaction, or literature checks that answer the same paper question.