Medplum MCP vs Puumed
A side-by-side look at the Medplum MCP and Puumed MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Medplum MCP for biology & bioinformatics work; choose Puumed for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Medplum MCP when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
Choose Puumed when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 41/100 · Fair | 40/100 · Fair |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 2,760 | 1 |
| Directory activity | 2 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | Not listed | Not listed |
| Full listing | View Medplum MCP | View Puumed |
Tools & capabilities
Medplum MCP tools
No tool names declared yet. Check the project README from the listing page.
Puumed tools
No tool names declared yet. Check the project README from the listing page.
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Medplum MCP
No confirmed install command for Medplum MCP yet — follow the setup steps linked from its listing page rather than a guessed package name.
Puumed
{
"mcpServers": {
"puumed": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-pubmed"
]
}
}
}