Borrowing it
Nothing to install: this file belongs to Jeny-Liu/claude-code-biology-research. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/Jeny-Liu/claude-code-biology-research/main/.claude/settings.jsongit clone --depth 1 https://github.com/Jeny-Liu/claude-code-biology-researchWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/settings/jeny-liu/claude-code-biology-research/settings)<a href="https://agentmods.dev/settings/jeny-liu/claude-code-biology-research/settings"><img src="https://agentmods.dev/badge/settings/jeny-liu/claude-code-biology-research/settings/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/settings/jeny-liu/claude-code-biology-research/settings"><img src="https://agentmods.dev/badge/settings/jeny-liu/claude-code-biology-research/settings.svg" alt="Reviewed on agentmods" width="80" height="20"></a>Grade A, and why
claude-code-biology-research scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
{
"mcpServers": {
"ncbi-biology": {
"command": "uvx",
"args": ["ncbi-mcp-server"],
"env": {
"NCBI_API_KEY": "${NCBI_API_KEY}",
"EMAIL": "${EMAIL}"
}
},
"pubmed-mcp": {
"command": "npx",
"args": ["-y", "pubmed-mcp-server"],
"env": {
"NCBI_API_KEY": "${NCBI_API_KEY}"
}
},
"uniprot-pdb": {
"command": "uvx",
"args": ["uniprot-mcp-server"]
},
"biopython-mcp": {
"command": "uvx",
"args": ["biopython-mcp-server"]
},
"r-bioconductor": {
"command": "uvx",
"args": ["r-bioc-mcp-server"]
},
"geo-sra": {
"command": "uvx",
"args": ["geo-mcp-server"],
"env": {
"NCBI_API_KEY": "${NCBI_API_KEY}"
}
},
"cheminfo": {
"command": "uvx",
"args": ["cheminformatics-mcp-server"]
}
},
"permissions": {
"allow": [
"bash",
"read",
"write",
"edit",
"glob",
"grep"
]
}
}
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2mo ago First seen · 53 lines scan A 6eea7eb6f400
claude-code-biology-research is a settings file published in the GitHub repository Jeny-Liu/claude-code-biology-research (2 stars, last pushed 4mo ago), licensed MIT. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other settings, from other repositories
supabase
Agent settings declaring 2 hook events (SessionStart, PostToolUse).
superset
Agent settings declaring 1 hook event (PreToolUse).
RuView
Agent settings declaring 8 hook events (PreToolUse, PostToolUse, UserPromptSubmit, SessionStart) and 4 allowed tools.
claude-cookbooks
Agent settings declaring 2 hook events (SessionStart, PreToolUse).
orm
Agent settings declaring 4 hook events (PreToolUse, PostToolUse, WorktreeCreate, Stop) and 21 allowed tools.
claude-code-best-practice
Agent settings declaring 30 hook events (PreToolUse, PermissionRequest, PostToolUse, PostToolUseFailure) and 24 allowed tools.