| FMRS | 65 / 100 · C | 75 / 100 · B |
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| Reliability | 9 / 20 | 12 / 20 |
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| Security and permissions | 13 / 20 | 16 / 20 |
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| Maintenance | 13 / 20 | 14 / 20 |
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| Documentation | 16 / 20 | 18 / 20 |
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| Setup experience | 14 / 20 | 15 / 20 |
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| Best for | - Researchers and biomedical agents needing programmatic PubMed or Europe PMC access
- Workflows requiring structured literature metadata, full text, and citation output
- Literature-management tasks involving DOI, PMID, and PMCID identifiers
| - Individuals or teams who prioritise privacy and offline operation and do not want data leaving the machine
- Users who share memory across multiple MCP clients such as Claude Code, Claude Desktop, Hermes Agent, OpenClaw, Cursor, Codex and Gemini CLI
- Scenarios that need encrypted storage, a hash-chained audit log and verifiable vault migration
- Users who want low-latency recall, a bundled embedding model and no extra LLM calls inside the memory layer
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| Not for | - Users seeking searches across non-biomedical databases
- Workflows requiring guaranteed full-text availability for every article
- Users that need this server to be treated as an official PubMed or NCBI server
| - Users who need cloud multi-device sync or a hosted team memory service; moving between machines means locking the vault and copying the file
- Users who expect the server itself to run an LLM that extracts facts and decides what to remember; Compartment explicitly keeps no LLM inside and leaves that to the host model
- Users who cannot keep a passphrase safe or who need a recovery path if it is lost, since Compartment never generates a password, seed or recovery phrase
- Deployments that require network transports such as SSE or streamable-http; this server is stdio only and opens no ports
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| Required permissions | - The server needs access to NCBI services; Europe PMC access is needed when Europe PMC features are enabled.
- Full-text fallback through Unpaywall requires UNPAYWALL_EMAIL and access to Unpaywall.
- API keys and contact emails are optional; NCBI_API_KEY can increase the NCBI rate limit.
- Streamable HTTP deployments can use none, jwt, or oauth authentication; the default is none.
| - Read and write the vault file under the user's home directory, by default ~/.compartment/memory.vault, and its sibling settings file
- Access the session directory holding the unlock credential (configurable with COMPARTMENT_SESSION_DIR), which also carries the shared embedding process's Unix socket
- Optionally use the macOS keychain (compartment unlock --keychain is an explicit opt-in, and it survives reboots)
- Write or merge an mcpServers entry into each MCP client's own configuration file, taking a byte-exact backup first
- Install a PostToolUse hook for Claude Code that captures memory files the agent writes
- Serve a read-only dashboard on 127.0.0.1 behind a one-time random URL token
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| Risks and side effects | - Full-text retrieval depends on PMC, Europe PMC, or legal open-access sources and may return unavailable or truncated results.
- Unpaywall results may include best-effort warnings and may be returned as HTML Markdown or PDF text.
- The source does not provide further details about authentication or availability of the public hosted instance.
- NCBI and Europe PMC requests are affected by rate limits, timeouts, and retry settings.
| - A leaked passphrase means the encrypted content can be decrypted; Compartment generates no recovery phrase and cannot recover a lost passphrase
- Enabling the memory_unlock tool places the passphrase in the model's context, which is why it is off by default
- If a 2FA keyfile is lost, for example a USB stick, the vault cannot be opened even with the passphrase
- `export --plaintext` writes the vault as unencrypted JSONL, so that file must be handled carefully
- Memory content can come from untrusted sources; recall wraps memories with a notice that they are stored data and content can be marked quarantined, but the host agent must still treat memory as data to limit prompt-injection risk
- The capture hook and client integration write into the user's own settings files, although the implementation backs up and merges rather than replacing
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| Supported clients | Claude Desktop, Cursor, VS Code | Claude Desktop, Claude Code, Hermes Agent, OpenClaw, Cursor, VS Code, Codex, Gemini CLI, Cline, Roo Code, Zed, OpenCode, LM Studio, AnythingLLM, BoltAI, Goose, Kiro |
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| Tools | 11 | 14 |
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