Biomcp MCP Server
by genomoncologyBioMCP: Biomedical Model Context Protocol
Biomcp is an open-source mcp server by genomoncology, written mainly in Rust, with 669 GitHub stars and the MIT license. Its code was last updated Oct 30, 2026.
Scan summary: scanned Nov 5, 2026 at commit 561d3fe. Seen able to read environment and secrets, connect to the internet. Scan policy
ScannedScanned. The automated checks below ran on the commit shown. Read each line for what was and was not covered.
Full scan at
561d3fe · Nov 5, 2026 ScannedStatic, secrets and dependency checks completed with no critical findings.
Warning. This check found something worth reading in the findings below. It is not proof of a problem.Static code scanwarnWarning. This check found something worth reading in the findings below. It is not proof of a problem.
Flagged. This check found an issue. See the findings below.Secrets scanfailFlagged. This check found an issue. See the findings below.
Flagged. This check found an issue. See the findings below.Dependency audit40 known vulnerabilitiesfailFlagged. This check found an issue. See the findings below.
Passed. This check ran and found nothing it flags.Manifestserver.jsonpassPassed. This check ran and found nothing it flags.
Flagged. This check found an issue. See the findings below.BuildfailFlagged. This check found an issue. See the findings below.
Not applicable. This check does not apply to this kind of project, or it was not run in this scan.Boot & handshaken/aNot applicable. This check does not apply to this kind of project, or it was not run in this scan.
Warning. This check found something worth reading in the findings below. It is not proof of a problem.Network egresswarnWarning. This check found something worth reading in the findings below. It is not proof of a problem.
Not applicable. This check does not apply to this kind of project, or it was not run in this scan.Reproducible (×3)n/aNot applicable. This check does not apply to this kind of project, or it was not run in this scan.
Findings (39)
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.secrets issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dependencies issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dependencies issueDetails are available to the maintainer after claiming this listing.
- mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.calamine@0.36.1: 1 known vulnerabilityRUSTSEC-2026-0436
Cargo.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.quick-xml@0.39.2: 2 known vulnerabilitiesRUSTSEC-2026-0194, RUSTSEC-2026-0195
architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/rust_probe/Cargo.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.pulldown-cmark@0.13.4: 2 known vulnerabilitiesRUSTSEC-2026-0414, RUSTSEC-2026-0433
tools/alphagenome-proto-generator/Cargo.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Install or build failed in a clean environment
- mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Install contacted hosts other than package registriesreleases.astral.sh, static.rust-lang.org
- lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
sdlc/records/2146-refuse-an-empty-supplement-download-build.md:94 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
tests/article_asset_terminal.rs:624 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
tests/golden/cases/search-trial-melanoma-recruiting.json:8 - lowLow. Minor, or common in normal tools. Shown for information.block-buffer@0.12.0: 2 known vulnerabilitiesGHSA-qwgh-2vcv-g2f7, GHSA-qwgh-2vcv-g2f7
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.instant@0.1.13: 1 known vulnerabilityRUSTSEC-2024-0384
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.memmap2@0.5.10: 1 known vulnerabilityRUSTSEC-2026-0186
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.pin-utils@0.1.0: 1 known vulnerabilityRUSTSEC-2026-0441
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.tokio@1.50.0: 1 known vulnerabilityRUSTSEC-2026-0386
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.ttf-parser@0.25.1: 2 known vulnerabilitiesRUSTSEC-2026-0192, RUSTSEC-2026-0192
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.zstd@0.13.3: 1 known vulnerabilityRUSTSEC-2026-0391
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.zstd-safe@7.2.4: 12 known vulnerabilitiesRUSTSEC-2026-0395, RUSTSEC-2026-0396, RUSTSEC-2026-0397, RUSTSEC-2026-0398, RUSTSEC-2026-0399 +7 more
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.zstd-sys@2.0.16+zstd.1.5.7: 1 known vulnerabilityRUSTSEC-2026-0410
Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.anyhow@1.0.102: 1 known vulnerabilityRUSTSEC-2026-0190
architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/rust_probe/Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.crossbeam-epoch@0.9.18: 1 known vulnerabilityRUSTSEC-2026-0204
architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/rust_probe/Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.fxhash@0.2.1: 1 known vulnerabilityRUSTSEC-2025-0057
architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/rust_probe/Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.lzw@0.10.0: 1 known vulnerabilityRUSTSEC-2020-0144
architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/rust_probe/Cargo.lock - lowLow. Minor, or common in normal tools. Shown for information.Reads environment variables not listed in the manifestBIOMCP_BIN, OMIM_API_KEY, PHENOTYPE_SPIKE_USER_AGENT, PHENOTYPE_SPIKE_TIMEOUT, BIOMCP_MYCHEM_BASE, S2_API_KEY, TIKTOKEN_CACHE_DIR, BIOMCP_MCPB_CERTIFICATE, BIOMCP_MCPB_PRIVATE_KEY, BIOMCP_MCPB_CHAIN, GITHUB_JOB, GITHUB_REPOSITORY, GITHUB_WORKFLOW_REF, GITHUB_RUN_ID, GITHUB_RUN_ATTEMPT
Network activity
During install
files.pythonhosted.orgindex.crates.iopypi.orgreleases.astral.shstatic.crates.iostatic.rust-lang.org
While running
Not run — the code wasn't started in this scan
Automated result for the commit shown. See our scan policy. View the scan log
Maintainers can claim the listing to rescan, or dispute a result.
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