Three-Layer Memory System — automatic fact extraction, entity-based knowledge graph, and weekly synthesis. Manages life/areas/ entities with atomic facts and living summaries.
npx skills add https://github.com/jdrhyne/agent-skills --skill knowledge-graph
Maintain a lightweight, append-only entity graph that compounds durable facts across sessions.
Store the graph under:
<workspace>/life/areas/
people/<slug>/
companies/<slug>/
projects/<slug>/
Each entity folder should contain:
summary.md for the short, current snapshotfacts.jsonl for atomic, append-only factsUse one JSON object per line:
{
"id": "<slug>-NNN",
"fact": "Plain-English fact",
"category": "relationship|milestone|status|preference|context|decision",
"ts": "YYYY-MM-DD",
"source": "conversation|manual|inference",
"status": "active|superseded",
"supersedes": "<older-id>"
}
Durable facts usually include:
facts.jsonl.summary.md in 3 to 8 concise lines.summary.md first.facts.jsonl only if the summary is stale or the user asked for detail.Recall should be triggered, not automatic.
Create the core directories once:
mkdir -p life/areas/people life/areas/companies life/areas/projects
If multiple agents share one workspace, point them at the same life/ directory so they operate on the same entity store.
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.
Build and distribute Expo development clients locally or via TestFlight
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Take jdrhyne/knowledge-graph from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.