🧠 Digital Brain MCP

A Second Brain powered by Model Context Protocol (MCP), Google Gemini Embedding 2, and Supabase pgvector — deployed on Vercel.

Connect any MCP-compatible AI client (Claude, Cursor, OpenCode, Copilot, etc.) and give it persistent long-term memory. Store notes, code, research, decisions, and any knowledge — then recall it instantly with semantic search.

Architecture

AI Client (Claude / Cursor / OpenCode / Copilot)
        │
        ▼  MCP Protocol (Streamable HTTP + SSE)
        │  Authorization: Bearer <api-key>
┌──────────────────────────────┐
│   Vercel (Next.js)           │
│   /api/mcp/[transport]       │
│                              │
│   ┌── Auth Middleware ──┐    │
│   │  Bearer token check │    │
│   └─────────────────────┘    │
│                              │
│   Tools:                     │
│    • store_memory            │
│    • search_memory           │
│    • list_memories           │
│    • update_memory           │
│    • delete_memory           │
│    • get_stats               │
└──────────┬───────────────────┘
           │
     ┌─────┴─────┐
     ▼           ▼
┌─────────┐  ┌──────────────┐
│ Gemini  │  │  Supabase    │
│ Embed 2 │  │  PostgreSQL  │
│  API    │  │  + pgvector  │
└─────────┘  │  vector(768) │
             └──────────────┘

How It Works

1. You say (in Claude/Cursor/etc): "Remember that the EBR system uses Azure Functions for the API layer"
2. MCP client calls your Digital Brain's store_memory tool
3. Gemini Embedding 2 converts the text into a 768-dimension vector
4. Supabase stores the text + vector in PostgreSQL with pgvector
5. Later, you ask: "What tech does the EBR system use?"
6. search_memory embeds your query, runs cosine similarity search, returns the matching memory

Security Model

The server uses Bearer token authentication on every request:

• Fail-closed: If no API keys are configured, ALL requests are rejected
• Multi-key support: Set multiple comma-separated keys in DIGITAL_BRAIN_API_KEYS so each client gets its own key (and you can rotate independently)
• Row Level Security (RLS): Enabled on the Supabase memories table — only service_role can access data. The anon key has zero access.
• Service Role Key: Only stored server-side in Vercel env vars, never exposed to clients

Generating API Keys

# Generate a strong 256-bit key
openssl rand -hex 32

Tech Stack

Why 768 dimensions?

Gemini Embedding 2 outputs 3072 dimensions by default but supports Matryoshka Representation Learning (MRL) — you can truncate to 768 with minimal quality loss. This saves ~75% storage and makes queries significantly faster, which matters a lot more for a personal knowledge base than that last fraction of accuracy.

MCP Tools Reference

store_memory

Save a new piece of knowledge to the Digital Brain.

search_memory

Semantic search across everything stored. Your query is embedded and matched by cosine similarity.

list_memories

Browse memories with optional filters (no embedding needed).

update_memory

Modify an existing memory. If content changes, a new embedding is generated automatically.

delete_memory

Permanently remove a memory by ID.

get_stats

Get brain statistics: total count, breakdown by type, and top tags.

No parameters.

Setup Guide

Prerequisites

• Node.js 18+
• A Supabase account (free tier works)
• A Google AI Studio API key (free tier)
• A Vercel account (free Hobby plan works)

Step 1: Clone the Repo

git clone https://github.com/YOUR_USERNAME/digital-brain-mcp.git
cd digital-brain-mcp
npm install

Step 2: Set Up Supabase

1. Create a new Supabase project (or use an existing one)
2. Go to SQL Editor in the Supabase dashboard
3. Copy the contents of supabase/migrations/001_create_memories.sql
4. Paste and run the entire SQL script
5. This creates: the memories table, pgvector extension, HNSW index, search functions, RLS policies, and stat helpers

Get your credentials from Supabase → Settings → API:

• SUPABASE_URL — the Project URL
• SUPABASE_SERVICE_ROLE_KEY — the service_role secret (NOT the anon key)

Step 3: Get a Gemini API Key

1. Go to Google AI Studio
2. Create a new API key
3. Save it as GEMINI_API_KEY

Step 4: Generate Your MCP API Key

openssl rand -hex 32

Save the output as DIGITAL_BRAIN_API_KEYS.

Step 5: Local Development

# Create .env.local with your keys
cp .env.example .env.local
# Edit .env.local with your actual values

# Start the dev server
npm run dev

The MCP endpoint will be at http://localhost:3000/api/mcp/sse.

Step 6: Deploy to Vercel

1. Push the repo to GitHub
2. Import the project in Vercel
3. Set environment variables in Vercel dashboard:
   • DIGITAL_BRAIN_API_KEYS — your generated key(s)
   • GEMINI_API_KEY — your Google AI key
   • SUPABASE_URL — your Supabase project URL
   • SUPABASE_SERVICE_ROLE_KEY — your Supabase service role key
4. Create a KV (Redis) store: Vercel dashboard → Storage → Create KV Database
   • This auto-sets REDIS_URL
5. Set a firewall bypass for MCP: Settings → Security → Firewall → Add rule:
   • Condition: "Request path contains /api/mcp"
   • Action: "Bypass"
6. Deploy!

Your production MCP endpoint: https://digital-brain-mcp.vercel.app/api/mcp/sse

Connecting AI Clients

Claude Desktop / Claude Code

Add to your Claude MCP config (~/.claude/claude_desktop_config.json or project .mcp.json):

{
  "mcpServers": {
    "digital-brain": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://digital-brain-mcp.vercel.app/api/mcp/sse",
        "--header",
        "Authorization:Bearer YOUR_API_KEY_HERE"
      ]
    }
  }
}

Cursor

Go to Settings → Cursor Settings → Tools & MCP → Add Server:

• Type: SSE
• URL: https://digital-brain-mcp.vercel.app/api/mcp/sse
• Headers: Authorization: Bearer YOUR_API_KEY_HERE

OpenCode / Any MCP Client

Use the SSE endpoint https://digital-brain-mcp.vercel.app/api/mcp/sse with an Authorization: Bearer <key> header.

Perplexity / Computer

Connect via the MCP config pattern above, or access the Supabase database directly through an existing connector.

Project Structure

digital-brain-mcp/
├── src/
│   ├── app/
│   │   ├── api/
│   │   │   └── mcp/
│   │   │       └── [transport]/
│   │   │           └── route.ts    ← MCP endpoint (tools + auth)
│   │   ├── layout.tsx              ← Root layout
│   │   └── page.tsx                ← Landing page
│   └── lib/
│       ├── auth.ts                 ← Bearer token authentication
│       ├── embeddings.ts           ← Gemini Embedding 2 client
│       └── supabase.ts             ← Supabase client + data helpers
├── supabase/
│   └── migrations/
│       └── 001_create_memories.sql ← Full database schema
├── .env.example                    ← Template for environment variables
├── .mcp.json                       ← MCP client connection config
├── package.json
├── tsconfig.json
├── next.config.js
└── README.md                       ← This file

Example Usage

Once connected, you can say things like:

• "Remember that the Revvity Signals API uses OAuth 2.0 client credentials flow" → Calls store_memory with appropriate tags

• "What do I know about authentication patterns?" → Calls search_memory, finds semantically related memories

• "Show me all my code snippets" → Calls list_memories with content_type: "code"

• "How many memories do I have?" → Calls get_stats

Cost Estimate

For personal second-brain use, everything stays well within free tiers.

Future Enhancements

• Multimodal storage: Store images/PDFs directly (Gemini Embedding 2 supports them natively)
• Auto-tagging: Use an LLM to suggest tags for new memories
• Bulk import: CLI tool to import from Obsidian, Notion, or markdown files
• Scheduled embedding refresh: Re-embed old memories when the model improves
• Multi-user support: Add user_id column and JWT auth for shared deployments

License

MIT