Operon MCP Server

by swaruplab• 101•• Scanned•Claim this listing•Request removal
Research & Analysisbioinformaticsclaude aidesktop idegenomicshpc

AI-powered IDE for bioinformatics — built by biologists, for biologists

Operon is an open-source mcp server by swaruplab, written mainly in Python, with 101 GitHub stars and the MIT license. Its code was last updated Oct 11, 2026.

Scan summary: scanned Nov 5, 2026 at commit 313661c. Seen able to run shell commands, run dynamic code. Scan policy

Scanned
Full scan at 313661c · Nov 5, 2026
Scanned Builds
Static code scanwarn
Secrets scanpass
Dependency audit506 known vulnerabilitiesfail
Manifestnonewarn
Buildpass
Boot & handshaken/a
Network egressn/a
Reproducible (×3)n/a

Findings (138)

  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    code-execution issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dropper issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • high
    dependencies issue
    Details are available to the maintainer after claiming this listing.
  • medium
    Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    vite.config.ts:20
  • medium
    @xmldom/xmldom@0.8.13: 10 known vulnerabilities
    GHSA-27p8-2357-5qqv, GHSA-4w3w-2rp5-g8jm, GHSA-6gmq-8vp8-gcm6, GHSA-6h8r-xr42-gp59, GHSA-8344-3jmq-59r6 +5 more
    package-lock.json
  • medium
    brace-expansion@2.0.2: 7 known vulnerabilities
    GHSA-3jxr-9vmj-r5cp, GHSA-6j4f-fj2g-mc7p, GHSA-f886-m6hf-6m8v, GHSA-mh99-v99m-4gvg, GHSA-q2hr-2g5m-vwhr +2 more
    package-lock.json
  • medium
    browserslist@4.28.1: 2 known vulnerabilities
    GHSA-73wf-gq98-2v4g, GHSA-c83g-rgw3-j3cx
    package-lock.json
  • medium
    dompurify@3.2.7: 21 known vulnerabilities
    GHSA-39q2-94rc-95cp, GHSA-55q2-fjhq-7xh7, GHSA-6688-9rhm-gjv2, GHSA-76mc-f452-cxcm, GHSA-c2j3-45gr-mqc4 +16 more
    package-lock.json
  • medium
    dompurify@3.3.1: 21 known vulnerabilities
    GHSA-39q2-94rc-95cp, GHSA-55q2-fjhq-7xh7, GHSA-6688-9rhm-gjv2, GHSA-76mc-f452-cxcm, GHSA-c2j3-45gr-mqc4 +16 more
    package-lock.json
  • medium
    nanoid@3.3.11: 3 known vulnerabilities
    GHSA-28wg-ghj8-5hjv, GHSA-2v37-7h3g-55p8, GHSA-xwg4-73v4-xw9w
    package-lock.json
  • medium
    picomatch@2.3.1: 2 known vulnerabilities
    GHSA-3v7f-55p6-f55p, GHSA-c2c7-rcm5-vvqj
    package-lock.json
  • medium
    picomatch@4.0.3: 2 known vulnerabilities
    GHSA-3v7f-55p6-f55p, GHSA-c2c7-rcm5-vvqj
    package-lock.json
  • medium
    postcss@8.5.8: 4 known vulnerabilities
    GHSA-6g55-p6wh-862q, GHSA-fxqj-rqcc-2cmp, GHSA-qx2v-qp2m-jg93, GHSA-r28c-9q8g-f849
    package-lock.json
  • medium
    source-map-js@1.2.1: 1 known vulnerability
    GHSA-68fv-2mgg-jv7q
    package-lock.json
  • medium
    uuid@10.0.0: 1 known vulnerability
    GHSA-w5hq-g745-h8pq
    package-lock.json
  • medium
    vite@6.4.1: 9 known vulnerabilities
    GHSA-4w7w-66w2-5vf9, GHSA-587h-7wmj-h5pm, GHSA-698v-4r3x-3vcv, GHSA-9jrq-w75r-8gcw, GHSA-fx2h-pf6j-xcff +4 more
    package-lock.json
  • medium
    xlsx@0.18.5: 2 known vulnerabilities
    GHSA-4r6h-8v6p-xvw6, GHSA-5pgg-2g8v-p4x9
    package-lock.json
  • medium
    fsspec@2025.3.0: 1 known vulnerability
    PYSEC-2026-4217
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langchain@0.3.20: 2 known vulnerabilities
    PYSEC-2026-2192, PYSEC-2026-2555
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langchain-community@0.3.19: 1 known vulnerability
    PYSEC-2026-1515
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langchain-text-splitters@0.3.6: 2 known vulnerabilities
    PYSEC-2026-1520, PYSEC-2026-77
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langgraph-checkpoint@2.0.20: 3 known vulnerabilities
    PYSEC-2026-1527, PYSEC-2026-2573, PYSEC-2026-2574
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langgraph-checkpoint-sqlite@2.0.6: 5 known vulnerabilities
    PYSEC-2026-1528, PYSEC-2026-1529, PYSEC-2026-1530, PYSEC-2026-3636, GHSA-6hmw-9432-67qq
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langgraph-sdk@0.1.57: 2 known vulnerabilities
    PYSEC-2026-2575, PYSEC-2026-4240
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    langsmith@0.3.15: 3 known vulnerabilities
    PYSEC-2026-2582, PYSEC-2026-2583, GHSA-f4xh-w4cj-qxq8
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    msgpack@1.1.0: 2 known vulnerabilities
    PYSEC-2026-3625, GHSA-j586-36cw-2gc2
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    oauthlib@3.2.2: 3 known vulnerabilities
    PYSEC-2026-4113, PYSEC-2026-4114, GHSA-7984-qgvg-3j9c
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    orjson@3.10.15: 1 known vulnerability
    PYSEC-2026-107
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    protobuf@5.29.3: 2 known vulnerabilities
    PYSEC-2026-1805, PYSEC-2026-1806
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    pyasn1@0.6.1: 9 known vulnerabilities
    PYSEC-2026-1810, PYSEC-2026-2263, PYSEC-2026-3455, PYSEC-2026-3456, PYSEC-2026-3457 +4 more
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    setuptools@75.8.2: 3 known vulnerabilities
    PYSEC-2025-49, PYSEC-2026-3447, GHSA-xmj3-9gf7-h52w
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    soupsieve@2.6.0: 4 known vulnerabilities
    PYSEC-2026-3071, PYSEC-2026-3072, PYSEC-2026-4170, PYSEC-2026-4171
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    starlette@0.46.1: 7 known vulnerabilities
    PYSEC-2026-161, PYSEC-2026-1941, PYSEC-2026-1942, PYSEC-2026-2280, PYSEC-2026-2281 +2 more
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    urllib3@2.3.0: 8 known vulnerabilities
    PYSEC-2026-141, PYSEC-2026-1994, PYSEC-2026-1996, PYSEC-2026-1997, PYSEC-2026-1998 +3 more
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    wheel@0.45.1: 1 known vulnerability
    PYSEC-2026-2047
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • medium
    httpcore2@2.9.1: 2 known vulnerabilities
    PYSEC-2026-3844, PYSEC-2026-3844
    protocols/cellagent-annotation/repo/requirements.txt
  • medium
    httpx2@2.9.1: 10 known vulnerabilities
    PYSEC-2026-3845, PYSEC-2026-3846, PYSEC-2026-3847, PYSEC-2026-3848, PYSEC-2026-3849 +5 more
    protocols/cellagent-annotation/repo/requirements.txt
  • medium
    requests@2.9.2: 5 known vulnerabilities
    PYSEC-2018-28, PYSEC-2023-74, PYSEC-2026-1872, PYSEC-2026-1873, PYSEC-2026-2275
    protocols/clinical-note-summarization/requirements.txt
  • medium
    tqdm@4.9.0: 2 known vulnerabilities
    PYSEC-2017-74, PYSEC-2026-1976
    protocols/scrna-qc/requirements.txt
  • medium
    quick-xml@0.38.4: 2 known vulnerabilities
    RUSTSEC-2026-0194, RUSTSEC-2026-0195
    src-tauri/Cargo.lock
  • medium
    quick-xml@0.39.4: 2 known vulnerabilities
    RUSTSEC-2026-0194, RUSTSEC-2026-0195
    src-tauri/Cargo.lock
  • medium
    quinn-proto@0.11.14: 5 known vulnerabilities
    RUSTSEC-2026-0185, RUSTSEC-2026-0338, RUSTSEC-2026-0339, RUSTSEC-2026-0340, RUSTSEC-2026-0342
    src-tauri/Cargo.lock
  • medium
    rustls-webpki@0.103.11: 4 known vulnerabilities
    RUSTSEC-2026-0098, RUSTSEC-2026-0099, RUSTSEC-2026-0104, RUSTSEC-2026-0382
    src-tauri/Cargo.lock
  • medium
    tauri@2.10.3: 1 known vulnerability
    GHSA-7gmj-67g7-phm9
    src-tauri/Cargo.lock
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-ortholog-inference/examples/ortholog_analysis.py:33
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-ortholog-inference/examples/ortholog_analysis.py:113
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-synteny-analysis/examples/synteny_analysis.py:58
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-synteny-analysis/examples/synteny_analysis.py:59
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-synteny-analysis/examples/synteny_analysis.py:65
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/comparative-genomics-synteny-analysis/examples/synteny_analysis.py:81
  • low
    In tests/examples/docs: Deserializes data with pickle/marshal, which can execute code.
    protocols/genome-engineering-off-target-prediction/examples/off_target_analysis.py:56
  • low
    In tests/examples/docs: Deserializes data with pickle/marshal, which can execute code.
    protocols/genome-engineering-off-target-prediction/examples/off_target_analysis.py:58
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/liquid-biopsy-cfdna-preprocessing/examples/preprocess_cfdna.py:32
  • low
    In tests/examples/docs: Runs shell commands. Fine for some tools, but it means the agent can run anything your user can.
    protocols/liquid-biopsy-ctdna-mutation-detection/examples/detect_ctdna_mutations.py:35
  • low
    Possible example credential in docs/tests: curl-auth-user
    src-tauri/protocols/benchling-integration/references/api_endpoints.md:24
  • low
    Possible example credential in docs/tests: curl-auth-header
    src-tauri/protocols/benchling-integration/references/api_endpoints.md:31
  • low
    Possible example credential in docs/tests: curl-auth-header
    3 matches in this file
    src-tauri/protocols/benchling-integration/references/authentication.md:112
  • low
    Possible example credential in docs/tests: curl-auth-user
    2 matches in this file
    src-tauri/protocols/benchling-integration/references/authentication.md:36
  • low
    Possible example credential in docs/tests: curl-auth-header
    6 matches in this file
    src-tauri/protocols/protocolsio-integration/references/additional_features.md:31
  • low
    Possible example credential in docs/tests: curl-auth-header
    3 matches in this file
    src-tauri/protocols/protocolsio-integration/references/discussions.md:44
  • low
    Possible example credential in docs/tests: curl-auth-header
    4 matches in this file
    src-tauri/protocols/protocolsio-integration/references/protocols_api.md:45
  • low
    Possible example credential in docs/tests: curl-auth-header
    7 matches in this file
    src-tauri/protocols/protocolsio-integration/references/file_manager.md:41
  • low
    Possible example credential in docs/tests: generic-api-key
    2 matches in this file
    src-tauri/protocols/reactome-database/references/api_reference.md:163
  • low
    Possible example credential in docs/tests: curl-auth-header
    3 matches in this file
    src-tauri/protocols/protocolsio-integration/references/workspaces.md:32
  • low
    @babel/core@7.29.0: 1 known vulnerability
    GHSA-4x5r-pxfx-6jf8
    package-lock.json
  • low
    baseline-browser-mapping@2.10.9: 1 known vulnerability
    GHSA-w5vr-8v7q-w6rv
    package-lock.json
  • low
    echarts@5.6.0: 1 known vulnerability
    GHSA-fgmj-fm8m-jvvx
    package-lock.json
  • low
    postcss-selector-parser@6.1.2: 2 known vulnerabilities
    GHSA-rj75-hqrm-r3gf, GHSA-w9m9-85wc-3x92
    package-lock.json
  • low
    pygments@2.19.1: 2 known vulnerabilities
    PYSEC-2026-2987, PYSEC-2026-2987
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    filelock@3.18.0: 4 known vulnerabilities
    PYSEC-2026-1374, PYSEC-2026-1375, GHSA-69hj-f68j-2879, GHSA-8mx5-7m5m-r77g
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    fonttools@4.56.0: 1 known vulnerability
    PYSEC-2026-1389
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    idna@3.10.0: 1 known vulnerability
    PYSEC-2026-215
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    langchain-openai@0.3.8: 1 known vulnerability
    PYSEC-2026-76
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    marshmallow@3.26.1: 1 known vulnerability
    PYSEC-2026-1605
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    opentelemetry-api@1.31.0: 1 known vulnerability
    GHSA-xcq7-p3pf-p88h
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    python-dotenv@1.0.1: 1 known vulnerability
    PYSEC-2026-2270
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    requests@2.32.3: 2 known vulnerabilities
    PYSEC-2026-1872, PYSEC-2026-2275
    protocols/automated-bioinformatics-pipelines/repo/requirements.txt
  • low
    opentelemetry-api@1.9.1: 2 known vulnerabilities
    GHSA-xcq7-p3pf-p88h, GHSA-xcq7-p3pf-p88h
    protocols/cellagent-annotation/repo/requirements.txt
  • low
    scikit-learn@1.2.2: 1 known vulnerability
    PYSEC-2024-110
    protocols/trialgpt-matching/repo/requirements.txt
  • low
    tqdm@4.65.0: 1 known vulnerability
    PYSEC-2026-1976
    protocols/trialgpt-matching/repo/requirements.txt
  • low
    anyhow@1.0.102: 1 known vulnerability
    RUSTSEC-2026-0190
    src-tauri/Cargo.lock
  • low
    event-listener@5.4.1: 1 known vulnerability
    RUSTSEC-2026-0221
    src-tauri/Cargo.lock
  • low
    fxhash@0.2.1: 1 known vulnerability
    RUSTSEC-2025-0057
    src-tauri/Cargo.lock
  • low
    glib@0.18.5: 1 known vulnerability
    RUSTSEC-2024-0429
    src-tauri/Cargo.lock
  • low
    libz-sys@1.1.28: 1 known vulnerability
    RUSTSEC-2026-0418
    src-tauri/Cargo.lock
  • low
    pin-utils@0.1.0: 1 known vulnerability
    RUSTSEC-2026-0441
    src-tauri/Cargo.lock
  • low
    proc-macro-error@1.0.4: 1 known vulnerability
    RUSTSEC-2024-0370
    src-tauri/Cargo.lock
  • low
    rand@0.7.3: 1 known vulnerability
    RUSTSEC-2026-0097
    src-tauri/Cargo.lock
  • low
    rand@0.8.5: 1 known vulnerability
    RUSTSEC-2026-0097
    src-tauri/Cargo.lock
  • low
    rustls@0.23.38: 4 known vulnerabilities
    RUSTSEC-2026-0285, RUSTSEC-2026-0346, RUSTSEC-2026-0348, RUSTSEC-2026-0349
    src-tauri/Cargo.lock
  • low
    serde_with@3.18.0: 1 known vulnerability
    GHSA-7gcf-g7xr-8hxj
    src-tauri/Cargo.lock
  • low
    serial@0.4.0: 1 known vulnerability
    RUSTSEC-2017-0008
    src-tauri/Cargo.lock
  • low
    tar@0.4.45: 1 known vulnerability
    GHSA-3pv8-6f4r-ffg2
    src-tauri/Cargo.lock
  • low
    tokio@1.51.1: 1 known vulnerability
    RUSTSEC-2026-0386
    src-tauri/Cargo.lock
  • low
    unic-char-property@0.9.0: 1 known vulnerability
    RUSTSEC-2025-0081
    src-tauri/Cargo.lock
  • low
    unic-char-range@0.9.0: 1 known vulnerability
    RUSTSEC-2025-0075
    src-tauri/Cargo.lock
  • low
    unic-common@0.9.0: 1 known vulnerability
    RUSTSEC-2025-0080
    src-tauri/Cargo.lock
  • low
    unic-ucd-ident@0.9.0: 1 known vulnerability
    RUSTSEC-2025-0100
    src-tauri/Cargo.lock
  • low
    unic-ucd-version@0.9.0: 1 known vulnerability
    RUSTSEC-2025-0098
    src-tauri/Cargo.lock
  • low
    webpki-root-certs@1.0.6: 1 known vulnerability
    RUSTSEC-2026-0383
    src-tauri/Cargo.lock
  • low
    webpki-roots@1.0.6: 1 known vulnerability
    RUSTSEC-2026-0381
    src-tauri/Cargo.lock
  • low
    zbus_names@3.0.0: 1 known vulnerability
    RUSTSEC-2026-0371
    src-tauri/Cargo.lock
  • low
    zstd-safe@5.0.2+zstd.1.5.2: 9 known vulnerabilities
    RUSTSEC-2026-0395, RUSTSEC-2026-0397, RUSTSEC-2026-0399, RUSTSEC-2026-0400, RUSTSEC-2026-0401 +4 more
    src-tauri/Cargo.lock
  • low
    zstd-sys@2.0.16+zstd.1.5.7: 1 known vulnerability
    RUSTSEC-2026-0410
    src-tauri/Cargo.lock
  • low
    zvariant@4.2.0: 1 known vulnerability
    RUSTSEC-2026-0370
    src-tauri/Cargo.lock
  • low
    zvariant_derive@4.2.0: 1 known vulnerability
    RUSTSEC-2026-0372
    src-tauri/Cargo.lock
  • low
    No manifest declaring network access and environment variables (agent.json)
  • low
    Couldn't work out how to start the server. Set "entrypoint" in agent.json.

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