Menu
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
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.
| 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."
