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Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
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Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.
Explain where project data and outputs live (e.g. GPFS, data/, predictions/) from knowledge base.
Baseado na classificação ocupacional SOC
| name | cache_to_knowledge |
| description | Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup). |
| category | bio/literature |
| version | 1 |
| requires_tools | ["write_file"] |
| requires_network | false |
| user_invocable | true |
| species | any |
| modality | literature |
| stage | utilities |
| stability | experimental |
| safety_level | low |
User or agent has just fetched content (e.g. abstract, gene summary) and wants to save it to the knowledge base for future use.
Path: Use path knowledge/cache/{source}/{id}.md (sanitize id for filename). If path provided and under knowledge/, use it.
Content: Format as Markdown: title, source, id, date (optional), then content. Keep under 50k chars.
Write: Use write_file with path under knowledge/ and the composed content.
Confirm: Tell user "Cached to knowledge/cache/... . You can retrieve it later via search_knowledge_base."
