Updated October 2026
Build a local-first AI second brain
A second brain is the notes system you trust more than your memory. Adding AI to it should mean an assistant that reads your notes, links them, answers questions from them and files what it learns back in, without moving everything into someone else's cloud. With CoWork OS your notes stay as plain Markdown files in a folder you own, and they open in Obsidian or any editor.
The two pieces
1. A research vault for knowledge. CoWork OS ships an LLM wiki workflow, inspired by Andrej Karpathy's idea of an LLM-maintained knowledge base. It keeps raw sources, builds durable linked notes on top of them, and uses Obsidian-style [[wikilinks]]:
research/wiki/
index.md ← map of everything
inbox.md ← things to process
concepts/ ← one note per idea
entities/ ← people, companies, tools
projects/
queries/ ← saved answers to questions you asked
raw/articles/ ← original sources, never edited
raw/papers/
outputs/ ← slides and charts made from the vault
2. Memory for you. Separately, the memory folder keeps what the agent learns about your preferences and projects, also as Markdown in a local git repo.
Set it up
- Install CoWork OS and connect a model. For private notes, use a local model.
- Choose a workspace folder. It can be your existing notes folder.
- Start the vault:
/llm-wiki my reading notes --mode init
To use a folder you already have, point it there with --path, which can be relative to the workspace or absolute:
/llm-wiki my reading notes --mode init --path /Users/you/Notes/Research
- Add sources: "Ingest these three articles and the PDF in Downloads", or
/llm-wiki --mode ingest. - Ask questions. In query mode the agent answers from the vault first, then saves the answer back as a note in
queries/, so your second brain grows from your own questions.
Keep it healthy
| Mode | What it does |
|---|---|
ingest | Captures sources and updates notes |
query | Answers from the vault and saves the answer back |
lint | Checks links, structure and contradictions |
refresh | Re-checks important notes against newer sources |
Raw sources are never edited after capture, and the agent asks before rewriting more than ten notes at once. Schedule a weekly lint or refresh with scheduled tasks.
Works with Obsidian
The vault is ordinary Markdown with [[wikilinks]], so Obsidian opens it as-is. By default CoWork OS doesn't create an .obsidian settings folder; turn that on with --obsidian on if you want one. You can also show the vault on the CoWork OS home screen: Settings → Appearance → Home widgets → Show research vault.
Why local-first matters here
A second brain holds your most personal thinking. Keeping it as files on your disk means you can read it without the app, back it up however you like, move it to another tool, and choose whether any model outside your computer ever sees it. LLM wiki documentation
Frequently asked questions
Can I use AI with my Obsidian vault?
Yes. CoWork OS works on plain Markdown folders with [[wikilinks]], so it can build and maintain notes that Obsidian opens directly. Point it at an existing folder with --path.
Does the AI write back into my notes?
Yes, when you ask it to. Ingest mode updates notes from new sources, and query mode saves answers back into the vault. Raw sources are never edited, and it asks before rewriting more than ten notes.
Can an AI second brain stay private?
Yes. The notes stay on your computer as Markdown files, and with a local model through Ollama or MLX nothing is sent to a cloud provider.
What is an LLM wiki?
A knowledge base that an AI agent maintains: raw sources are kept unchanged, and the agent writes linked notes, indexes and summaries on top of them. CoWork OS ships one as a built-in workflow.
CoWork OS itself is free and open source. Model providers, gateways, connected services, and account plans may charge separately and apply their own eligibility and usage rules.
Last reviewed 2026-10-23 against official documentation. Features, plans and prices change; check the linked sources before deciding. CoWork OS is not affiliated with Obsidian.