🧬 Enzyme

Enzyme compiles your notes and other knowledge sources into a local index that:

1. Uses temporally grounded context sampling that captures the contextual use of tags and wikilinks, or natural accumulation in folders (i.e. pseudo-Zettelkasten)
2. With this context, it "dreams" questions in the background (called catalysts) and embeds them. At query time, each question finds its nearest docs, so it avoid needing to "dream" full summaries. (see note)
3. Keeps refreshing, but separates new doc ingestion (local, fast) from catalyst evolution (cheap, periodic)

The catalysts help orient the agent to the wiki. Enzyme saves up to 50% tokens vs. plain agentic search with grep.

(Note: your system may already generate lots of memories in different buckets; Enzyme catalysts help thread them together)

Get started

Open your Markdown notes folder with your agent and paste this prompt.

Set up Enzyme for the Markdown notes folder I have open. If you cannot identify it, ask me for its path.

Install Enzyme if needed using https://raw.githubusercontent.com/byenzyme/enzyme/main/install.sh, and install the instructions for this agent. Read and follow the installed enzyme-workspace-setup skill.

Use it to suggest settings from my notes and prepare search. Show me what you propose to include or exclude, and let me correct it before building the local search index.

Then answer one useful question using my notes, with links to the sources, and suggest a question I can ask next. Keep my existing notes in place and unchanged. Ask separately before any cleanup, model download, or recurring task.

After setup, keep working with your agent as usual. The new guidance tells your agent how to use Enzyme and when to refresh it.

Prefer to install it yourself first? Run this, then paste the same prompt:

curl -fsSL https://raw.githubusercontent.com/byenzyme/enzyme/main/install.sh | bash
cd /path/to/your/notes
enzyme install claude # or: codex, hermes, openclaw

What it's for

Enzyme was built for knowledge bases that grow quickly:

• Obsidian vaults that accumulate dated notes in a few folders
• Meeting notes and AI-native, Markdown CRM setups
• Agent memory written as Markdown

At setup time, it proposes a .enzyme program by reading your wiki and existing agent instructions, like:

profile relationships {
  seek "what matters between people"
  notice ["meaningful exchanges", "shared interests", "unfinished conversations"]
}

workspace "notes" {
  source markdown "notes" { path "~/notes" }

  question budget 40
  sample across time
  favor recent periods

  learn questions from folder "people"
    including linked pages
    about relationships
  learn questions from folder "meetings" about operational
  learn questions from tags ["startup", "design"] about decisions
  learn questions from folder "inbox"

  project questions into "~/notes/Readwise"

  // Guidance compiled for your agent, not an enforced hook.
  when asked {
    "Use grep for names, titles, and exact phrases."
    retrieve passages through learned questions
    answer with sources
  }
}

And you can give feedback to modify the program.

Enzyme helps most when a question spans many notes written over time: context for a decision on a project, or a broader theme arising from conversations with one person. It's designed to support knowledge captures that might be later be important, even if they don't serve a current task. Enzyme is focused on doing one thing well: giving agents the tools to make ideas compound. And it ships with a set of profiles designed around a personal knowledge base were refined over 2 years of personal use:

Read...	For...	Profile
Project notes	what's stuck and what keeps blocking	operational
Decision records	why a choice won, what would change it	decision_trace
Saved articles	connections to what you're already working on	resonance_trace
Journals	what keeps returning across entries	reflective
People notes	what matters in these relationships	relational
Feedback / activity logs	what works for you, under what constraints	preference_evidence
(default)	costs, assumptions, live tensions	tension_trace

Reference

Setup without an agent

enzyme compile -v
# Review the .enzyme settings file at the path printed by compile.
enzyme init --quiet
enzyme doctor
enzyme catalyze "a question about your notes"

compile proposes settings and saves them; init builds the local index from them; doctor reports what was indexed and any problems.

Other sources

For Apple Notes, a preset builds a named workspace program from your Notes database. Review the saved .enzyme program before running init:

enzyme --workspace apple-notes compile --preset apple-notes \
  "$HOME/Library/Group Containers/group.com.apple.notes/NoteStore.sqlite"
enzyme --workspace apple-notes init

This is the beginning of the README. Read the rest at the original. Read the full README ↗