second-brain MCP

Name: second-brain MCP
Author: ddmanyes

by ddmanyesversion 0.1.0i★ –iRuns on your computer

Registry nameio.github.ddmanyes/mcp-second-brain

Install

Overview

Description from the maker (original English)

Self-maintaining knowledge vault: figure-level search, auto-wikilinks, and memory compression.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Search & AI memory

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
The registry lists no key to fill in.

You need

PyPIPython’s uv installed (for the uvx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "second-brain": {
      "command": "uvx",
      "args": [
        "mcp-second-brain"
      ]
    }
  }
}

Run this in your terminal

claude mcp add second-brain -- uvx mcp-second-brain

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "second-brain": {
      "command": "uvx",
      "args": [
        "mcp-second-brain"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "second-brain": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "mcp-second-brain"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 7, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account ddmanyes, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Search & AI memoryi

More stars than 0% of the other 7258 servers in this category
Published to the registry more recently than 14% of the other 7258 servers in this category
Basic checks equal to or better than 100% of the other 7258 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is second-brain MCP safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.1.0) reached the registry 5 months ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Python (uv) on your computer.

What can I use instead?

In the same category: Context7, Codebase Memory, Exa

Alternatives

Servers in the same category from other makers, sorted by stars.

Reading a card:★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

Context7

by upstash

Feeds AI the latest docs for libraries and frameworks before it answers, so code it writes does not use outdated, removed functions.

Computer or cloud★ 64,224MITUpdated today

Install

Codebase Memory

by DeusData

Codebase knowledge graph for AI agents — 162 languages, sub-ms queries, 99% fewer tokens.

Runs on your computer★ 48,148MITUpdated 20 days ago

Install

Exa

by exa-labs

Connect AI agents to Exa for web search, content fetching, and multi-step research.

Runs in the cloud★ 5,213MITUpdated last month

Install

README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

second-brain MCP Server

A self-maintaining personal knowledge base for AI agents — a plain-Markdown vault, powered by MCP.

📖 English · 繁體中文

A local knowledge base your AI agent can read, write, and maintain on its own. Save a paper or note with one command — second-brain converts it to Markdown, OCRs every figure, embeds it for semantic search, and auto-links it to related notes. Notes you stop reading compress themselves over time, so recall stays cheap as the vault grows.

Everything is plain Markdown — sync via Google Drive / iCloud / git, switch agents anytime, zero lock-in.

Highlights

One command saves anything — save_article(url_or_pdf) fetches, converts to Markdown, OCRs figures (Claude Vision), embeds, and auto-links.
Figure-level search — search_figures("UMAP melanocyte") returns the exact panel across your whole library.
Self-organizing — new notes auto-link to related ones; frequently-read notes extract reusable rules.
Memory that forgets like a brain — Ebbinghaus ranking; stale notes auto-compress (60–90% fewer tokens).
Read-only housekeeping audit — inspect article metadata, links, exact duplicate candidates, inbox age, and source freshness without changing the vault.
Session continuity — get_context() reloads goals + top notes + rules at the start of every session.
Pluggable backend — DuckDB (default, offline) or Postgres + pgvector (central, multi-machine). Self-hosted embeddings optional; BM25 fallback when offline.

Quick Start (Claude Code)

pip install mcp-second-brain

playwright install chromium

claude mcp add --scope user second-brain \ --env SECOND_BRAIN_PATH=~/second-brain \ -- python -m mcp_second_brain

The vault directory and templates are created on first run. Then tell your agent init_vault to verify.

⚠️ PyPI currently lags the source tree. For the newest build — plus Claude Desktop, Windows, and multi-machine / central-server setups — see [NEW_MACHINE_SETUP.md](NEW_MACHINE_SETUP.md).

Core Tools

Tool	What it does
`auth_context`	Read the authenticated caller's canonical UUID, role, and RBAC state
`get_context`	Session start — goals + top-ranked notes + auto-rules
`save_article`	URL / PDF → Markdown + figures + embeddings
`search_notes` / `search_figures`	Hybrid BM25 + semantic search (note text / figure content)
`search_articles`	Structured author, ORCID, DOI/PMID/PMCID and year search for papers
`audit_article_records`	Bounded, read-only article housekeeping and social-source freshness report
`new_note` / `update_note` / `append_to_note`	Create & edit notes (auto-filed, auto-indexed, auto-linked)
`vault_sleep`	Compress old, low-activity notes
`get_agent_instructions`	Serve the full filing SOP (AGENTS.md) to remote agents

Full tool reference (46 tools) lives in [AGENTS.md](AGENTS.md).

Use search_notes when you need content, health_check when the server or index may be unhealthy, and audit_article_records when you need a housekeeping report. Audit results never merge, archive, or delete notes automatically.

How It Works

Any source (paper · PDF · web · note)

│ save_article · new_note ▼ Markdown vault ──► index (DuckDB, or Postgres + pgvector) 00-inbox/ • BM25 + semantic search 10-projects/ • figure OCR + vision descriptions 20-areas/ • auto-wikilinks between related notes 30-resources/ • Ebbinghaus ranking → weekly auto-compression decisions/ memory/ │ ▼ Your AI agent queries it — search_notes · search_figures · get_context

The vault is the source of truth; the index is rebuildable anytime (sync_index). Filing conventions live in one operating manual — AGENTS.md — served to any agent via get_agent_instructions(), so every agent files things the same way without being re-taught.

Vault Structure

vault/

├── 00-inbox/ Unprocessed captures ├── 10-projects/ Active projects ├── 20-areas/ Ongoing research / coding domains ├── 30-resources/ Papers & articles (save_article writes here) ├── 40-archive/ Auto-compressed originals ├── decisions/ Architecture Decision Records ├── memory/ goals.md · rules.md (injected every session) └── templates/ Note templates

Legacy author metadata

search_articles reads structured frontmatter, so older article notes without authors are not guessed from body text or references. A bounded two-phase CLI can prepare those notes safely: first create and review a manifest, then apply it separately.

python -m mcp_second_brain.author_backfill \

--vault " " --limit 20 --out /tmp/author-backfill.json python -m mcp_second_brain.author_backfill \ --vault " " --apply --manifest /tmp/author-backfill.json

Apply on the central writer host only. Each entry requires an exact DOI/PMID/PMCID or title match and unchanged content/body hashes; successful writes are reindexed.

Documentation

[AGENTS.md](AGENTS.md) — filing SOP, naming conventions, full tool reference (single source of truth)
[NEW_MACHINE_SETUP.md](NEW_MACHINE_SETUP.md) — source install, self-hosting, multi-machine central server, API keys
[CONTEXT.md](CONTEXT.md) — domain model / ubiquitous language

Design Notes

Inspired by biological memory: the Ebbinghaus forgetting curve (access_count / ln(age_days)) for ranking, and sleep-dependent consolidation (weekly LLM compression of low-access notes). Built with MarkItDown · DuckDB · pgvector · FastMCP · Playwright · Claude API.

second-brain MCP

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Search & AI memoryi

Common questions

Alternatives

Context7

Codebase Memory

Exa

README from the maker

second-brain MCP Server

Highlights

Quick Start (Claude Code)

Core Tools

How It Works

Vault Structure

Legacy author metadata

Documentation

Design Notes

License