Sandwalk: An agent harness for ambitious work.

Featured MCP servers, local Omnigraph stdio MCP, and Cursor-style ~/.sandwalk/mcp.json definitions.

Dashboard MCP servers list and </> Edit mcp.json action

Dashboard → MCPs (/dashboard/mcp) manages Model Context Protocol (MCP) servers stored in ~/.sandwalk/mcp.json. Sandwalk uses the standard Cursor / Claude Desktop mcpServers JSON format, so you can paste any Cursor mcp.json configuration directly into Sandwalk (or copy Sandwalk's mcp.json into Cursor).

Featured MCP Servers

Sandwalk seeds a curated catalog of scientific, molecular visualization, knowledge-graph, and research MCP servers in Dashboard → MCPs:

Omnigraph

stdio · local

Local Lance-backed knowledge graph engine (v0.13.0) with typed .pg ontologies, hybrid BM25/vector RRF search, and Git-style branching.

ModernRelay/omnigraph ↗

PyMOL

stdio · local bridge

Control a live commercial or open-source PyMOL session — load structures, build selections, align pockets, and render ray-traced figures.

agentic-pymol plugin ↗

RayMol

stdio · Apple Silicon Metal

Drive RayMol (Metal-accelerated molecular viewer for macOS) — fetch structures, change representations, and capture the viewport.

raymol.io ↗

Tamarind Bio

http · API key

Protein design, structure prediction (AlphaFold, Boltz, Chai), molecular docking, and MD simulations on Tamarind Bio.

mcp.tamarind.bio ↗

Paperclip

http · OAuth / API key

Search and synthesize 11M+ biomedical papers, FDA regulatory docs, clinical trials, and UniProt / PDB / ChEMBL records.

paperclip.gxl.ai ↗

Latch Bio

http · OAuth

Bioinformatics workflows, single-cell/spatial data management, and cloud compute on the Latch platform.

mcp.latch.bio ↗

Neurosnap

http · API key

Cloud biology suite for protein folding, docking, antibody design, and ADMET/toxicity prediction jobs.

neurosnap.ai ↗

Hugging Face

http · HF_TOKEN

Search Hub models, datasets, Spaces, papers, and documentation, and invoke community Gradio tools.

huggingface.co/mcp ↗

Exa Search

http · OAuth / API key

Neural web search and page extraction for scientific papers, patents, molecules, and technical documentation.

mcp.exa.ai ↗

Tavily

http · OAuth / API key

Real-time web search, grounding, and structured content extraction for research agents.

mcp.tavily.com ↗

Linear

http · OAuth / API key

Create and query issues, projects, cycles, and comments for engineering and research operations.

mcp.linear.app ↗

Cursor-Style `mcp.json` Structure (`~/.sandwalk/mcp.json`)

Click </> Edit mcp.json in the top-right corner of Dashboard → MCPs (or open ~/.sandwalk/mcp.json in any editor) to inspect or edit all configured servers in one JSON file:

Editing ~/.sandwalk/mcp.json directly inside Dashboard -> MCPs

Example `~/.sandwalk/mcp.json`

{
  "mcpServers": {
    "omnigraph": {
      "command": "/Users/you/.sandwalk/bin/sandwalk-omnigraph-mcp",
      "args": [],
      "type": "stdio",
      "description": "Local Omnigraph v0.13.0 knowledge graph engine (7 tools: query, upsert_node, record_claim, branch, load_cookbook_seed, sync_bundle).",
      "_sandwalkCatalogId": "omnigraph"
    },
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/Users/you/Projects"],
      "type": "stdio",
      "description": "Local filesystem MCP server via npx."
    },
    "latch": {
      "url": "https://mcp.latch.bio/mcp",
      "type": "http",
      "description": "Bioinformatics workflows, data, and compute on the Latch platform.",
      "_sandwalkCatalogId": "latch"
    },
    "custom-remote-mcp": {
      "url": "https://mcp.example.com/mcp",
      "type": "http",
      "headers": {
        "Authorization": "Bearer YOUR_TOKEN"
      },
      "disabled": false,
      "description": "Custom Streamable HTTP MCP server with custom headers."
    },
    "linear": {
      "url": "https://mcp.linear.app/mcp",
      "type": "http",
      "disabled": true,
      "description": "Issues, projects, and comments for product and ops workflows.",
      "_sandwalkCatalogId": "linear"
    }
  }
}

`mcpServers` Entry Field Reference

Every key under "mcpServers" is the server's identifier ("omnigraph", "latch", "linear", or any custom name):

Field	Type	Required	Description
`type`	`"stdio"` \| `"http"` \| `"sse"`	Optional	Transport protocol. Inferred automatically as `"stdio"` when `command` is present, or `"http"` (Streamable HTTP) when `url` is present. Use `"sse"` for legacy Server-Sent Events endpoints.
`command`	`string`	For `stdio`	Executable name or absolute path (e.g., `"npx"`, `"uvx"`, `"python3"`, or `"/Users/you/.sandwalk/bin/sandwalk-omnigraph-mcp"`).
`args`	`string[]`	Optional	Command-line arguments passed to `command` (defaults to `[]`).
`url`	`string`	For `http` / `sse`	Remote MCP endpoint URL (e.g., `"https://mcp.latch.bio/mcp"`).
`headers`	`Record<string, string>`	Optional	Custom HTTP headers (such as `Authorization: Bearer ...`) for custom remote servers.
`disabled`	`boolean`	Optional	Set to `true` to keep the server in `mcp.json` while disabling it at runtime. (`"enabled": true/false` is also accepted when pasting.)
`description`	`string`	Optional	Human-readable summary shown on the server card in Dashboard → MCPs.
`_sandwalkCatalogId`	`string`	Optional	Links a catalog-seeded entry (`omnigraph`, `latch`, `tamarind`, `neurosnap`, `paperclip`, `linear`, etc.) to Sandwalk's built-in catalog metadata and Dashboard → Integrations credential store so OAuth tokens and API keys are never written in plaintext into `mcp.json`.

Using MCPs in the CLI & Composer

In the Composer: Click + → MCP to toggle which MCP servers are active for the current session, or attach specific MCP servers to a Specialist profile (Dashboard → Specialists).
From the CLI:
```
sandwalk mcp list
```
Or type /mcps inside interactive sandwalk to connect, enable, validate, add, or remove MCP servers.

MCPs

Featured MCP Servers

Cursor-Style mcp.json Structure (~/.sandwalk/mcp.json)

Example ~/.sandwalk/mcp.json

mcpServers Entry Field Reference

Using MCPs in the CLI & Composer

On this page

Cursor-Style `mcp.json` Structure (`~/.sandwalk/mcp.json`)

Example `~/.sandwalk/mcp.json`

`mcpServers` Entry Field Reference