ToolUniverse AI Agent
by mims-harvardDemocratizing AI scientists with ToolUniverse
ToolUniverse is an open-source ai agent by mims-harvard, written mainly in Python, with 1,768 GitHub stars and the Apache-2.0 license. Its code was last updated Nov 1, 2026.
Scan summary: scanned Nov 5, 2026 at commit 5a0eaeb. Seen able to run dynamic code, 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
5a0eaeb · Nov 5, 2026 ScannedStatic, secrets and dependency checks completed with no critical findings. BuildsIt installed from a fresh machine.
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 audit1327 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.
Passed. This check ran and found nothing it flags.BuildpassPassed. This check ran and found nothing it flags.
Flagged. This check found an issue. See the findings below.Boot & handshakefailFlagged. 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.Network egressn/aNot applicable. This check does not apply to this kind of project, or it was not run in this scan.
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 (107)
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.dropper issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.credential-access issueDetails are available to the maintainer after claiming this listing.
- highHigh. Something risky that needs a close look before you install.credential-access 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.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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.Deserializes data with pickle/marshal, which can execute code.
src/tooluniverse/cache/sqlite_backend.py:88 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Contacts a hard-coded IP address instead of a domain name.
src/tooluniverse/cellmarker_tool.py:39 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Deserializes data with pickle/marshal, which can execute code.
src/tooluniverse/compose_scripts/tool_graph_composer.py:427 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Turns off TLS certificate checking, allowing traffic interception.
src/tooluniverse/euhealth/euhealth_live.py:175 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Turns off TLS certificate checking, allowing traffic interception.
src/tooluniverse/euhealth/euhealth_live.py:195 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Turns off TLS certificate checking, allowing traffic interception.
src/tooluniverse/euhealth/euhealth_live.py:218 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Turns off TLS certificate checking, allowing traffic interception.
src/tooluniverse/pheweb_phewas_tool.py:38 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Deserializes data with pickle/marshal, which can execute code.
src/tooluniverse/tdc_oracle_tool.py:108 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Deserializes data with pickle/marshal, which can execute code.
src/tooluniverse/tdc_oracle_tool.py:122 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.Deserializes data with pickle/marshal, which can execute code.
src/tooluniverse/tool_graph_web_ui.py:169 - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.torch@2.9.1: 20 known vulnerabilitiesPYSEC-2026-139, PYSEC-2026-2286, GHSA-qfhq-4f3w-5fph, GHSA-rrmf-rvhw-rf47, PYSEC-2026-139 +15 more
src/tooluniverse/remote/borzoi/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.tqdm@4.9.0: 26 known vulnerabilitiesPYSEC-2017-74, PYSEC-2026-1976, PYSEC-2017-74, PYSEC-2026-1976, PYSEC-2017-74 +21 more
src/tooluniverse/remote/cell2location/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.jinja2@3.0.3: 5 known vulnerabilitiesPYSEC-2026-1471, PYSEC-2026-1472, PYSEC-2026-1473, PYSEC-2026-1474, PYSEC-2026-1475
src/tooluniverse/remote/cellrank/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.setuptools@9.1.0: 12 known vulnerabilitiesPYSEC-2022-43012, PYSEC-2025-49, PYSEC-2026-1918, PYSEC-2026-3447, PYSEC-2022-43012 +7 more
src/tooluniverse/remote/chrombpnet/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.accelerate@1.9.0: 1 known vulnerabilityPYSEC-2026-3804
src/tooluniverse/remote/enformer/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.transformers@5.9.0: 1 known vulnerabilityPYSEC-2026-3929
src/tooluniverse/remote/enformer/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.gdown@5.2.1: 1 known vulnerabilityPYSEC-2026-2158
src/tooluniverse/remote/immune_compass/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.requests@2.9.2: 5 known vulnerabilitiesPYSEC-2018-28, PYSEC-2023-74, PYSEC-2026-1872, PYSEC-2026-1873, PYSEC-2026-2275
src/tooluniverse/remote/immune_compass/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.torch@2.10.0: 2 known vulnerabilitiesPYSEC-2026-139, GHSA-rrmf-rvhw-rf47
src/tooluniverse/remote/immune_compass/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.protobuf@3.9.2: 8 known vulnerabilitiesPYSEC-2022-48, PYSEC-2026-1805, PYSEC-2026-1806, PYSEC-2026-899, PYSEC-2022-48 +3 more
src/tooluniverse/remote/scanvi/requirements.txt - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.azure-core@1.36.0: 1 known vulnerabilityPYSEC-2026-1208
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.dnspython@2.8.0: 1 known vulnerabilityGHSA-45c3-73f7-pv4m
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.flask@2.1.3: 2 known vulnerabilitiesPYSEC-2023-62, PYSEC-2026-2151
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.fsspec@2025.9.0: 1 known vulnerabilityPYSEC-2026-4217
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.graphql-core@3.2.6: 2 known vulnerabilitiesGHSA-r77w-qph3-7vf8, GHSA-vj8h-fx38-h3vc
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.joserfc@1.7.4: 2 known vulnerabilitiesGHSA-9pg5-8c7x-5hfx, GHSA-jpxq-7h8p-2q76
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.lxml@6.0.1: 1 known vulnerabilityPYSEC-2026-87
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.mcp@1.29.0: 4 known vulnerabilitiesGHSA-5h93-6whr-6q8j, GHSA-84m7-p3x7-pcfv, GHSA-rwrf-2pqf-9j8j, GHSA-w4fh-qvv9-3v23
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.orjson@3.11.3: 1 known vulnerabilityPYSEC-2026-107
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.pip@25.3: 5 known vulnerabilitiesPYSEC-2026-1796, PYSEC-2026-196, PYSEC-2026-2875, PYSEC-2026-2876, PYSEC-2026-3721
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.protobuf@5.29.5: 1 known vulnerabilityPYSEC-2026-1805
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.pyarrow@23.0.0: 1 known vulnerabilityPYSEC-2026-113
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.pyasn1@0.6.1: 9 known vulnerabilitiesPYSEC-2026-1810, PYSEC-2026-2263, PYSEC-2026-3455, PYSEC-2026-3456, PYSEC-2026-3457 +4 more
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.soupsieve@2.8: 4 known vulnerabilitiesPYSEC-2026-3071, PYSEC-2026-3072, PYSEC-2026-4170, PYSEC-2026-4171
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.torch@2.8.0: 8 known vulnerabilitiesPYSEC-2025-203, PYSEC-2025-204, PYSEC-2025-206, PYSEC-2026-139, PYSEC-2026-2286 +3 more
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.urllib3@2.5.0: 6 known vulnerabilitiesPYSEC-2026-141, PYSEC-2026-1994, PYSEC-2026-1996, PYSEC-2026-1998, PYSEC-2026-4175 +1 more
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.virtualenv@20.34.0: 20 known vulnerabilitiesPYSEC-2026-2009, PYSEC-2026-4011, PYSEC-2026-4012, PYSEC-2026-4013, PYSEC-2026-4014 +15 more
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.werkzeug@2.3.8: 7 known vulnerabilitiesPYSEC-2026-2043, PYSEC-2026-2044, PYSEC-2026-2045, PYSEC-2026-2046, PYSEC-2026-2320 +2 more
uv.lock - mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.MCP server didn't complete the protocol handshakeserver exited early with code 2
- lowLow. Minor, or common in normal tools. Shown for information.In tests/examples/docs: Executes dynamically built code (eval / exec).
examples/mcp/mcp_server_test.py:12 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
examples/fourdn_examples.py:120 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key2 matches in this file
tests/tools/test_nvidia_nim_tool.py:35 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
tests/tools/test_return_schema_data_shapes.py:69 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key
tests/unit/test_gtdb_search_relevance.py:18 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key5 matches in this file
tests/unit/test_metabolomics_spectra_depth.py:68 - lowLow. Minor, or common in normal tools. Shown for information.Possible example credential in docs/tests: generic-api-key2 matches in this file
tests/unit/test_variant_prediction_scores_depth.py:105 - lowLow. Minor, or common in normal tools. Shown for information.idna@3.9.0: 10 known vulnerabilitiesPYSEC-2026-215, PYSEC-2026-215, PYSEC-2026-215, PYSEC-2026-215, PYSEC-2026-215 +5 more
docs/requirements.txt - lowLow. Minor, or common in normal tools. Shown for information.biopython@1.86: 1 known vulnerabilityPYSEC-2026-1221
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.fastmcp@3.4.5: 1 known vulnerabilityGHSA-7xgj-8392-5q4r
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.fastmcp-slim@3.4.5: 1 known vulnerabilityGHSA-7xgj-8392-5q4r
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.filelock@3.19.1: 4 known vulnerabilitiesPYSEC-2026-1374, PYSEC-2026-1375, GHSA-69hj-f68j-2879, GHSA-8mx5-7m5m-r77g
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.fonttools@4.59.2: 1 known vulnerabilityPYSEC-2026-1389
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.h2@4.3.0: 1 known vulnerabilityPYSEC-2026-3628
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.hpack@4.1.0: 1 known vulnerabilityPYSEC-2026-4053
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.idna@3.10: 1 known vulnerabilityPYSEC-2026-215
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.opentelemetry-api@1.44.0: 1 known vulnerabilityGHSA-xcq7-p3pf-p88h
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.pygments@2.19.2: 1 known vulnerabilityPYSEC-2026-2987
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.pytest@8.4.2: 1 known vulnerabilityPYSEC-2026-1845
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.python-dotenv@1.1.1: 1 known vulnerabilityPYSEC-2026-2270
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.requests@2.32.5: 1 known vulnerabilityPYSEC-2026-2275
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.setuptools@80.9.0: 2 known vulnerabilitiesPYSEC-2026-3447, GHSA-xmj3-9gf7-h52w
uv.lock - lowLow. Minor, or common in normal tools. Shown for information.Reads environment variables not listed in the manifestAZURE_OPENAI_ENDPOINT, AZURE_OPENAI_API_VERSION, CLAUDE_BIN, EVAL_MODEL, TOOLUNIVERSE_PLUGIN_DIR, CODEX_BIN, BENCH_JUDGE_WORKERS, BENCH_JUDGE_SUBSAMPLE, BENCH_JUDGE_VALIDATION, BENCH_JUDGE_INCREMENTAL, TOOLUNIVERSE_REPO, BENCH_EMBED_MODEL, BENCH_GEN_MODEL, BENCH_JUDGE_MODEL, BENCH_LLM_FINDER_MODEL
Network activity
During install
files.pythonhosted.orgpypi.org
While running
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