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Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). 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Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.","author":"","version":"","license":"MIT","overallGrade":"C","badgeStatus":"flagged","publishedAt":"2026-09-10T21:06:22.214Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/generate-image","findings":[{"id":"cmuxilnx50r84ad07jcuj397n","source":"vettd","category":"security","label":"Base64-decoded content stored in variable","detail":"Detected in scripts/generate_image.py:510 — `content = base64.b64decode(payload, validate=True)`","severity":"high","ruleId":"VTD-0025"},{"id":"cmuxilnx50r85ad07fwnmo38u","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxilnx50r86ad07ee4k2feg","source":"cisco","category":"security","label":"Code makes network requests","detail":"SKILL.md — Skill code makes network requests. 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Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.","author":"","version":"1.5","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:06:22.198Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/cellxgene-census","findings":[{"id":"cmuximwg50smlad077v9d50h1","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T07:10:40.370Z","lastVerifiedAt":"2026-10-22T07:10:40.370Z","lastChangeDetectedAt":"2026-10-06T08:48:24.278Z","scannedHash":"d990c5ef2bfe956ca30872e060872e0ed7c81263","latestUpstreamHash":"d990c5ef2bfe956ca30872e060872e0ed7c81263","nextCheckDueAt":"2026-10-23T08:54:50.323Z"}},{"id":"cmuxio16s0tx1ad07sxfc8hr4","slug":"dask","publicId":"64b4fb03-d236-46c1-97f4-64973e12a465","name":"dask","description":"Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunking, schedulers, and distributed diagnostics. 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Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2. For single-cell data use scanpy; for statistical fitting alone use pydeseq2.","author":"","version":"2.0","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:06:22.105Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/bulk-rnaseq","findings":[{"id":"cmuxihm8u0lioad07njsc8942","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T01:09:39.417Z","lastVerifiedAt":"2026-10-22T01:09:39.417Z","lastChangeDetectedAt":"2026-10-06T03:46:24.225Z","scannedHash":"c236cf85b07184ddb9cca999b1040f27b166ebbf","latestUpstreamHash":"c236cf85b07184ddb9cca999b1040f27b166ebbf","nextCheckDueAt":"2026-10-22T23:14:22.498Z"}},{"id":"cmuxiubc411mgad078wdv3957","slug":"deeptools","publicId":"082258a0-6307-4b23-88d4-7ced263e75d6","name":"deeptools","description":"NGS analysis toolkit. 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Use when implementing or debugging astronomical data analysis code with Astropy.","author":"","version":"1.5","license":"BSD-3-Clause license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:06:22.002Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/astropy","findings":[{"id":"cmuxipfc50vyead07taas1k4s","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T03:18:39.555Z","lastVerifiedAt":"2026-10-22T03:18:39.555Z","lastChangeDetectedAt":"2026-10-06T11:42:24.313Z","scannedHash":"fdecbcd876f0492da1e7c539735a7ce4fc9d253e","latestUpstreamHash":"fdecbcd876f0492da1e7c539735a7ce4fc9d253e","nextCheckDueAt":"2026-10-23T04:00:41.535Z"}},{"id":"cmuxilf740qodad0796kdgtka","slug":"statistical-power","publicId":"4688f5cd-eec9-43b8-a808-7b0aac60be29","name":"statistical-power","description":"Calculates sample sizes and statistical power for study planning. 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Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.","author":"","version":"1.3","license":"BSD-3-Clause license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:51.813Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/aeon","findings":[{"id":"cmuxio1oq0tykad0788jokk1x","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T02:40:39.513Z","lastVerifiedAt":"2026-10-22T02:40:39.513Z","lastChangeDetectedAt":"2026-10-06T10:24:24.295Z","scannedHash":"4cce1063a14400094c240a973ed70e2ef15889ae","latestUpstreamHash":"4cce1063a14400094c240a973ed70e2ef15889ae","nextCheckDueAt":"2026-10-23T03:54:01.150Z"}},{"id":"cmuxinyv10tktad07xnkd9ixc","slug":"scientific-brainstorming","publicId":"c6008832-2cee-42aa-8257-7c76d3ac7ca0","name":"scientific-brainstorming","description":"Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. 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Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.","author":"","version":"1.5","license":"Unknown","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.698Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/phylogenetics","findings":[{"id":"cmuxinz6i0tlsad07beyl6ivk","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T12:45:51.095Z","lastVerifiedAt":"2026-10-22T12:45:51.095Z","lastChangeDetectedAt":"2026-10-06T10:35:24.297Z","scannedHash":"28bdeba2d091247153b5f3d3eebd481a2bdff6bc","latestUpstreamHash":"28bdeba2d091247153b5f3d3eebd481a2bdff6bc","nextCheckDueAt":"2026-10-23T11:45:10.051Z"}},{"id":"cmuxiiqx00mvbad07cxrnb2t9","slug":"molfeat","publicId":"b2819cff-4da9-43e6-b48b-b7103863db67","name":"molfeat","description":"Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. 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Uses persistent hypotheses, isolated experiments, evidence propagation and held-out candidate comparison for multi-experiment research runs. Includes a standard-library state manager and guidance for the RUC-NLPIR Arbor CLI.","author":"","version":"1.6","license":"MIT license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.692Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/arbor","findings":[{"id":"cmuxiqtqb0xpzad07c834byqn","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/tree.py:144 — `f\"Use --force to overwrite (this erases the current run).\"`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxiqtqb0xq0ad07p4jf9jkk","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T16:26:38.060Z","lastVerifiedAt":"2026-10-22T16:26:38.060Z","lastChangeDetectedAt":"2026-10-06T13:05:24.328Z","scannedHash":"eac719629edd8df483c5061e0acfaa763d317d9c","latestUpstreamHash":"eac719629edd8df483c5061e0acfaa763d317d9c","nextCheckDueAt":"2026-10-23T14:21:06.731Z"}},{"id":"cmuxinxkc0tcnad07dljs4hrq","slug":"bioservices","publicId":"dc585534-f9a5-46e8-a7b1-0cf786d87d7d","name":"bioservices","description":"Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. 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Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs.","author":"","version":"1.4","license":"Apache-2.0","overallGrade":"F","badgeStatus":"flagged","publishedAt":"2026-09-10T21:05:46.297Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/nextflow","findings":[{"id":"cmuxikg9x0pf0ad07izyinp8b","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxikg9x0pf1ad07dpune1sx","source":"cisco","category":"security","label":"Remote fetch followed by execution","detail":"SKILL.md:31 — Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern.","severity":"critical","ruleId":"VTD-0090"},{"id":"cmuxikg9x0pf2ad071f48ittc","source":"cisco","category":"security","label":"Remote fetch followed by execution","detail":"SKILL.md:43 — Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern.","severity":"critical","ruleId":"VTD-0090"},{"id":"cmuxikg9x0pf3ad07l17r6yid","source":"cisco","category":"security","label":"Remote fetch followed by execution","detail":"references/testing.md:26 — Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern. (found in documentation — may be instructional)","severity":"medium","ruleId":"VTD-0090"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"F","criticalCount":2,"highCount":2}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T10:26:40.720Z","lastVerifiedAt":"2026-10-22T10:26:40.720Z","lastChangeDetectedAt":"2026-10-08T10:37:35.646Z","scannedHash":"7db04133e61f17f5d839eeba9ef026575a87d2a7","latestUpstreamHash":"7db04133e61f17f5d839eeba9ef026575a87d2a7","nextCheckDueAt":"2026-10-23T08:55:56.493Z"}},{"id":"cmuxis6a30zflad07iqdplmeu","slug":"matplotlib","publicId":"62c99750-9ba4-46e0-93d7-f0ba5e9f4d51","name":"matplotlib","description":"Creates and customizes scientific plots with Matplotlib. Used for fine-grained control over plot elements, novel plot types, and scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.","author":"","version":"1.4","license":"https://github.com/matplotlib/matplotlib/tree/main/LICENSE","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.207Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/matplotlib","findings":[{"id":"cmuxis6a30zfmad07pmcfpu94","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T04:37:39.637Z","lastVerifiedAt":"2026-10-22T04:37:39.637Z","lastChangeDetectedAt":"2026-10-06T23:52:15.687Z","scannedHash":"5878841efa26086ca904f5532fe057fdb20885e1","latestUpstreamHash":"5878841efa26086ca904f5532fe057fdb20885e1","nextCheckDueAt":"2026-10-23T05:45:49.447Z"}},{"id":"cmuxig42s0ko2ad07wnrb5pwu","slug":"cirq","publicId":"7b331ebd-10dc-419d-8ee3-7e43767c478f","name":"cirq","description":"Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.","author":"","version":"1.3","license":"Apache-2.0 license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.202Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/cirq","findings":[{"id":"cmuxig42s0ko3ad07yibqt9xr","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T04:33:39.630Z","lastVerifiedAt":"2026-10-22T04:33:39.630Z","lastChangeDetectedAt":"2026-10-06T02:30:24.208Z","scannedHash":"84ebcd0d15f6a27f56c50647b9194983531270e6","latestUpstreamHash":"84ebcd0d15f6a27f56c50647b9194983531270e6","nextCheckDueAt":"2026-10-23T05:57:31.437Z"}},{"id":"cmuxiqtsw0xqfad07n41ixm6s","slug":"pydeseq2","publicId":"1dee566b-e6d0-489c-9445-b23163a0f3e3","name":"pydeseq2","description":"Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.","author":"","version":"1.7","license":"MIT license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.200Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pydeseq2","findings":[{"id":"cmuxiqtsw0xqgad07kiem9u22","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T07:23:40.384Z","lastVerifiedAt":"2026-10-22T07:23:40.384Z","lastChangeDetectedAt":"2026-10-06T13:46:24.332Z","scannedHash":"6073e24b7a84d55a316a37d7dd24eb7a7536c351","latestUpstreamHash":"6073e24b7a84d55a316a37d7dd24eb7a7536c351","nextCheckDueAt":"2026-10-23T07:31:03.745Z"}},{"id":"cmuximydw0sqyad071lpmw6zg","slug":"shap","publicId":"a4c5c4b2-737c-4e27-aad0-4e03acc1ba16","name":"shap","description":"Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producing local or global SHAP visualizations.","author":"","version":"2.3","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:46.199Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/shap","findings":[{"id":"cmuximydw0sqzad0773hbryb4","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T18:36:00.480Z","lastVerifiedAt":"2026-10-22T18:36:00.480Z","lastChangeDetectedAt":"2026-10-06T08:23:24.275Z","scannedHash":"6bff165ee8d997a948ca4e88ccdc10b58f9e4a20","latestUpstreamHash":"6bff165ee8d997a948ca4e88ccdc10b58f9e4a20","nextCheckDueAt":"2026-10-23T18:11:43.047Z"}},{"id":"cmuxitf0u112cad07mifi0vqk","slug":"experimental-design","publicId":"217be49c-76a7-4c52-bf59-466b430cc2e2","name":"experimental-design","description":"Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone is planning a study, asks how to assign subjects/samples to groups, mentions randomization, blocking, stratification, controls, factorial or fractional-factorial designs, design of experiments (DOE), screening many factors, response-surface optimization, crossover or repeated-measures or split-plot designs, cluster/group randomization, Latin squares, plate layouts, batch/run-order effects, replication vs. pseudoreplication, or sequential/adaptive/group-sequential designs. Trigger even for informal phrasings like \"how should I set up this experiment\", \"how do I avoid confounding\", \"what's the best way to test these 6 factors\", or \"assign these mice to conditions\". For computing the sample size or power once the design is chosen, use statistical-power; for analyzing data already collected, use statistical-analysis.","author":"","version":"1.5","license":"MIT license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:42.202Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/experimental-design","findings":[{"id":"cmuxitf0u112dad07hcs74k62","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T07:45:40.466Z","lastVerifiedAt":"2026-10-22T07:45:40.466Z","lastChangeDetectedAt":"2026-10-07T02:08:15.929Z","scannedHash":"c4bc6dfbccdcc8452d6ea8ab9d7ce4e47b11f8b3","latestUpstreamHash":"c4bc6dfbccdcc8452d6ea8ab9d7ce4e47b11f8b3","nextCheckDueAt":"2026-10-23T08:44:17.697Z"}},{"id":"cmuxio1q20tyrad07l02q73m6","slug":"networkx","publicId":"739da861-8fe6-41a1-947e-feb276df3584","name":"networkx","description":"Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), reading/writing graph file formats, or drawing network topologies. Common applications include social, biological, transportation, and citation networks.","author":"","version":"1.4","license":"3-clause BSD license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:42.201Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/networkx","findings":[{"id":"cmuxio1q20tysad07naq4ta94","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T05:48:40.275Z","lastVerifiedAt":"2026-10-22T05:48:40.275Z","lastChangeDetectedAt":"2026-10-06T10:36:24.297Z","scannedHash":"0b8c72bafa3ed7b870a1ce0d0f8b23eac11b52ca","latestUpstreamHash":"0b8c72bafa3ed7b870a1ce0d0f8b23eac11b52ca","nextCheckDueAt":"2026-10-23T07:37:08.236Z"}},{"id":"cmuxit2g10ztsad0776l6ge19","slug":"rowan","publicId":"f2e26f63-9861-476c-adc0-ca318b8ca67a","name":"rowan","description":"Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.","author":"","version":"","license":"Proprietary (API key required)","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:42.200Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/rowan","findings":[{"id":"cmuxit2g20zttad07yqy6t25e","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T04:44:39.640Z","lastVerifiedAt":"2026-10-22T04:44:39.640Z","lastChangeDetectedAt":"2026-10-07T01:19:15.858Z","scannedHash":"192d8a347e8f44337daddd118bde77ff0a720008","latestUpstreamHash":"192d8a347e8f44337daddd118bde77ff0a720008","nextCheckDueAt":"2026-10-23T04:22:26.363Z"}},{"id":"cmuxikgcj0pffad07816gvu0z","slug":"tiledbvcf","publicId":"ae797b4a-b972-4a4c-99a9-733c1cbd1771","name":"tiledbvcf","description":"Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.","author":"","version":"1.3","license":"MIT license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:42.199Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/tiledbvcf","findings":[{"id":"cmuxikgck0pfgad07utv3c1vw","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T07:50:40.469Z","lastVerifiedAt":"2026-10-22T07:50:40.469Z","lastChangeDetectedAt":"2026-10-06T06:33:24.253Z","scannedHash":"d17312dd0336c9c6c91992c366840a418f61d33b","latestUpstreamHash":"d17312dd0336c9c6c91992c366840a418f61d33b","nextCheckDueAt":"2026-10-23T07:35:57.462Z"}},{"id":"cmuxiub9y11lyad074e2mw4a7","slug":"etetoolkit","publicId":"1ae296c2-5f56-4738-8bb5-35f5b58d9f66","name":"etetoolkit","description":"Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.","author":"","version":"3.0","license":"GPL-3.0-or-later","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:41.119Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/etetoolkit","findings":[{"id":"cmuxiub9y11lzad07zce5ftbz","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T19:27:00.568Z","lastVerifiedAt":"2026-10-22T19:27:00.568Z","lastChangeDetectedAt":"2026-10-07T02:47:39.890Z","scannedHash":"b0999ed6213cfd01acb2bbb08b8bc2acff0a6d82","latestUpstreamHash":"b0999ed6213cfd01acb2bbb08b8bc2acff0a6d82","nextCheckDueAt":"2026-10-23T20:31:21.099Z"}},{"id":"cmuxig4050knnad07yaq7k0v5","slug":"pymc","publicId":"0dd810d4-b832-4a69-9a9e-c1ef618a4080","name":"pymc","description":"Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model comparison. Use for probabilistic modeling and uncertainty inference in PyMC.","author":"","version":"2.0","license":"Apache License, Version 2.0","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:41.117Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pymc","findings":[{"id":"cmuxig4060knoad07mp72nsuk","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T01:47:39.461Z","lastVerifiedAt":"2026-10-22T01:47:39.461Z","lastChangeDetectedAt":"2026-10-06T02:49:24.213Z","scannedHash":"77cbb1dd10b5fc08d1f98ac2e05e13358cb2bdca","latestUpstreamHash":"77cbb1dd10b5fc08d1f98ac2e05e13358cb2bdca","nextCheckDueAt":"2026-10-23T03:49:31.824Z"}},{"id":"cmuximzmr0sxyad07t9fpwlfv","slug":"dnanexus-integration","publicId":"a8f68da3-2511-4925-8b86-bef2a4e0aa22","name":"dnanexus-integration","description":"Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Supports DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.","author":"","version":"2.3","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:37.790Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/dnanexus-integration","findings":[{"id":"cmuximzmr0sxzad072amxx0gq","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T04:11:39.608Z","lastVerifiedAt":"2026-10-22T04:11:39.608Z","lastChangeDetectedAt":"2026-10-06T08:56:24.278Z","scannedHash":"e81f4d414d086084bcb15ac0e9a6ff63f72e554c","latestUpstreamHash":"e81f4d414d086084bcb15ac0e9a6ff63f72e554c","nextCheckDueAt":"2026-10-23T06:34:26.983Z"}},{"id":"cmuxij36f0o09ad07jsgtk5bx","slug":"pathml","publicId":"1ef33bbb-eb6f-4991-8148-4ed94773cc1e","name":"pathml","description":"Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference. Use for whole-slide H&E, CODEX, Vectra, Mesmer, HoVer-Net, and HACTNet workflows.","author":"","version":"1.4","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:37.714Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pathml","findings":[{"id":"cmuxij36f0o0aad07u4pe0v9n","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/image_qc.py:261 — `synthetic.add_argument(\"--force\", action=\"store_true\")`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij36f0o0bad07pthbxxxj","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/plan_inference.py:271 — `parser.add_argument(\"--force\", action=\"store_true\")`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij36f0o0cad07gm7v1nd7","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/plan_pipeline.py:265 — `parser.add_argument(\"--force\", action=\"store_true\")`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij36f0o0dad07bfwp25ea","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/slide_manifest.py:370 — `validate.add_argument(\"--force\", action=\"store_true\")`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij36f0o0ead07durbyfo4","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/validate_spatial_schema.py:389 — `graph.add_argument(\"--force\", action=\"store_true\")`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij36f0o0fad07a1lgx9xi","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T04:15:39.612Z","lastVerifiedAt":"2026-10-22T04:15:39.612Z","lastChangeDetectedAt":"2026-10-06T04:55:24.238Z","scannedHash":"4b2909caffe95820fbcd3dc6c1066438b479ad4f","latestUpstreamHash":"4b2909caffe95820fbcd3dc6c1066438b479ad4f","nextCheckDueAt":"2026-10-23T06:03:53.931Z"}},{"id":"cmuxirtac0yd9ad07dn1abkwm","slug":"pathogen-variant-surveillance","publicId":"c1c7eb6a-ab4c-4eee-a2a4-eeecec4264f4","name":"pathogen-variant-surveillance","description":"Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage.","author":"","version":"1.3","license":"MIT","overallGrade":"C","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:37.713Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pathogen-variant-surveillance","findings":[{"id":"cmuxirtac0ydbad07aaoczfyt","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxirtac0ydcad073y11hp2y","source":"cisco","category":"security","label":"Code makes network requests","detail":"SKILL.md — Skill code makes network requests. 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Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation.","author":"","version":"1.4","license":"Unknown","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:35.292Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/glycoengineering","findings":[{"id":"cmuxiqjsa0x0zad07dzsa64n7","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxiqjsa0x10ad07fuwxucge","source":"cisco","category":"security","label":"Script contacts a destination the documentation never mentions","detail":"scripts/glytoucan_lookup.py:20 — Script contacts or configures 'purl.jp' but the skill documentation never visibly mentions it. 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Supports source ingestion (PDFs, web pages, audio, video, and Office documents), cited document chat, text and vector search, notes, custom transformations, and multi-speaker podcasts. Use when automating Open Notebook through its REST API or configuring its local or cloud AI providers, including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral.","author":"","version":"","license":"MIT","overallGrade":"C","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:34.619Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/open-notebook","findings":[{"id":"cmuxilmp20r2rad07lzc9ds43","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxilmp20r2sad071scmlxmo","source":"cisco","category":"security","label":"Potential description-behavior mismatch","detail":"SKILL.md — Skill performs actions not reflected in its description","severity":"medium","ruleId":"VTD-0087"},{"id":"cmuxilmp20r2tad07iklw27v9","source":"cisco","category":"security","label":"Sensitive source reaches a network sink","detail":"scripts/_common.py:29 — Correlated sensitive_environment → network behavior across scripts/_common.py.","severity":"high","ruleId":"CORRELATED_SENSITIVE_NETWORK_FLOW"},{"id":"cmuxilmp20r2uad073drm0rt4","source":"cisco","category":"security","label":"Outbound network request primitives that can transmit data externally","detail":"scripts/_common.py:29 — Pattern detected: requests.request(","severity":"medium","ruleId":"DATA_EXFIL_NETWORK_REQUESTS"},{"id":"cmuxilmp20r2vad07txj8qjj9","source":"cisco","category":"security","label":"Infinite loop without clear exit condition","detail":"scripts/source_ingestion.py:56 — Pattern detected: while True:","severity":"high","ruleId":"RESOURCE_ABUSE_INFINITE_LOOP"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"C","criticalCount":0,"highCount":2}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T00:43:07.011Z","lastVerifiedAt":"2026-10-22T00:43:07.011Z","lastChangeDetectedAt":"2026-10-06T07:58:24.270Z","scannedHash":"a08a2b48758589018d86ee5a38e8ff3c63a1b971","latestUpstreamHash":"a08a2b48758589018d86ee5a38e8ff3c63a1b971","nextCheckDueAt":"2026-10-23T01:31:49.267Z"}},{"id":"cmuxis59l0zcgad07sbyr9d3i","slug":"scvi-tools","publicId":"efe5c84f-8a51-4c1c-8a85-23bd31545d3f","name":"scvi-tools","description":"Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. 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Use this skill for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.","author":"","version":"","license":"MIT","overallGrade":"F","badgeStatus":"flagged","publishedAt":"2026-09-10T21:05:24.273Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/omero-integration","findings":[{"id":"cmuxitdne10xtad07mc3cugbm","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxitdne10xuad07cw8qttvx","source":"cisco","category":"security","label":"Direct socket connection to external server","detail":"scripts/validate_config.py:56 — Pattern detected: socket.getaddrinfo(","severity":"critical","ruleId":"DATA_EXFIL_SOCKET_CONNECT"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"F","criticalCount":1,"highCount":1}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T01:00:13.127Z","lastVerifiedAt":"2026-10-22T01:00:13.127Z","lastChangeDetectedAt":"2026-10-07T02:23:15.950Z","scannedHash":"95fa3c90eb6daeecca9f6c67fb9986741eeac44c","latestUpstreamHash":"95fa3c90eb6daeecca9f6c67fb9986741eeac44c","nextCheckDueAt":"2026-10-23T00:41:47.640Z"}},{"id":"cmuxihu980manad074t6olm1s","slug":"genomic-coordinates","publicId":"7dbd1d29-dec9-4f74-8bf6-b46105893e66","name":"genomic-coordinates","description":"Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include \"off by one\", \"0-based\", \"1-based\", \"half-open\", \"coordinate system\", \"left-align\", \"normalize variant\", \"bcftools norm\", \"chr prefix\", \"wrong genome build\", \"liftover\", \"REF mismatch\", and \"HGVS\".","author":"","version":"1.3","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:23.923Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/genomic-coordinates","findings":[{"id":"cmuxihu990maoad07w40fr184","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxihu990mapad07yty2k68k","source":"cisco","category":"security","label":"Code uses search/grep patterns but Grep tool not in allowed-tools","detail":"SKILL.md — Skill restricts tools to ['Read', 'Write', 'Edit', 'Bash'] but code uses regex search patterns","severity":"low","ruleId":"VTD-0087"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T02:35:39.508Z","lastVerifiedAt":"2026-10-22T02:35:39.508Z","lastChangeDetectedAt":"2026-10-06T04:02:24.230Z","scannedHash":"7eae514a4b7f93b6cb788cc1ba482dd46e9d0b48","latestUpstreamHash":"7eae514a4b7f93b6cb788cc1ba482dd46e9d0b48","nextCheckDueAt":"2026-10-23T04:24:44.046Z"}},{"id":"cmuxilnxa0r8ead076soc3t9u","slug":"seaborn","publicId":"ebe6da1b-e6d1-4fd0-bb81-78ec9145823e","name":"seaborn","description":"Creates Seaborn statistical visualizations with pandas integration for distributions, relationships, categorical comparisons, regression displays, pair plots, and heatmaps. 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Best suited to static exploratory plots; plotly covers interactive figures and scientific-visualization covers publication styling.","author":"","version":"1.5","license":"BSD-3-Clause license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:23.899Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/seaborn","findings":[{"id":"cmuxilnxb0r8fad07cvk4fxo3","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T01:43:39.456Z","lastVerifiedAt":"2026-10-22T01:43:39.456Z","lastChangeDetectedAt":"2026-10-06T07:51:24.266Z","scannedHash":"0013bbb60d4b21e7203f3739c96f4a40db15f086","latestUpstreamHash":"0013bbb60d4b21e7203f3739c96f4a40db15f086","nextCheckDueAt":"2026-10-22T23:39:19.714Z"}},{"id":"cmuximx0n0soaad070oi27mod","slug":"liteparse","publicId":"9dc003e7-c62f-4f4e-bd95-f46a31de67ac","name":"liteparse","description":"Local document and PDF parsing that returns spatial text with bounding boxes. 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Distinguishing capabilities are spatial text boxes, Markdown, page raster output, and local parsing with optional custom HTTP OCR.","author":"","version":"1.6","license":"Apache-2.0","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:23.898Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/liteparse","findings":[{"id":"cmuximx0n0sobad074c56wzut","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuximx0n0socad07t0k3gcnn","source":"cisco","category":"security","label":"Code uses glob/file patterns but Glob tool not in allowed-tools","detail":"SKILL.md — Skill restricts tools to ['Read', 'Write', 'Edit', 'Bash'] but code uses glob patterns","severity":"low","ruleId":"VTD-0087"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-21T22:16:01.621Z","lastVerifiedAt":"2026-10-21T22:16:01.621Z","lastChangeDetectedAt":"2026-10-06T09:12:24.279Z","scannedHash":"59a85c5672492a479f7780ac1d4c96ae2dc4f1d6","latestUpstreamHash":"59a85c5672492a479f7780ac1d4c96ae2dc4f1d6","nextCheckDueAt":"2026-10-22T23:21:59.114Z"}},{"id":"cmuxij1jr0nupad07wqlbrdyp","slug":"get-available-resources","publicId":"2ad95336-9411-4b32-bb99-153bbd857f49","name":"get-available-resources","description":"Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload. Produces a redacted JSON snapshot and conservative planning helpers without stress tests or assuming visible host hardware is usable.","author":"","version":"1.5","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:23.897Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/get-available-resources","findings":[{"id":"cmuxij1js0nuqad07yfex2qwq","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/_common.py:93 — `f\"{destination.name} already exists; use --force to replace it\"`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij1js0nurad07fhbd49ev","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/accelerator_diagnostics.py:127 — `\"--force\",`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij1js0nusad07n3gu4w26","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/detect_resources.py:1862 — `\"--force\",`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij1js0nutad074yv1grgu","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/plan_workload.py:289 — `\"--force\",`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij1js0nuuad07koxk1uww","source":"vettd","category":"security","label":"Safety bypass flag detected","detail":"Detected in scripts/snapshot_tools.py:464 — `\"--force\",`","severity":"low","ruleId":"VTD-0028"},{"id":"cmuxij1js0nuvad07g7t1u5on","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T02:25:39.498Z","lastVerifiedAt":"2026-10-22T02:25:39.498Z","lastChangeDetectedAt":"2026-10-06T05:30:24.241Z","scannedHash":"453a1104846c6e1c2a89a961682278621e4d3108","latestUpstreamHash":"453a1104846c6e1c2a89a961682278621e4d3108","nextCheckDueAt":"2026-10-23T04:29:49.612Z"}},{"id":"cmuxikfpn0pbbad078g679yey","slug":"histolab","publicId":"138dd57e-b735-459d-8ce3-944a8c7e2c83","name":"histolab","description":"Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile extraction, H&E stain normalization, and tile dataset preparation. For multiplexed imaging or deep learning inference pipelines, use pathml.","author":"","version":"1.5","license":"Apache-2.0 license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:23.882Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/histolab","findings":[{"id":"cmuxikfpn0pbcad07ze5xe0fc","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T05:11:39.864Z","lastVerifiedAt":"2026-10-22T05:11:39.864Z","lastChangeDetectedAt":"2026-10-06T06:25:24.253Z","scannedHash":"2e58534e47512cdbacb3c2b18e8a166242553098","latestUpstreamHash":"2e58534e47512cdbacb3c2b18e8a166242553098","nextCheckDueAt":"2026-10-23T03:07:25.203Z"}},{"id":"cmuxis5cc0zcwad07ldsbpfks","slug":"pennylane","publicId":"7c6b1b02-774f-4c44-9205-fcf9c8823a79","name":"pennylane","description":"Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum algorithms, quantum machine learning, simulator validation, and moving validated circuits to provider plugins. 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Use for literature reviews, evidence synthesis, and finding experimental details beyond abstracts.","author":"","version":"1.3","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:17.433Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/bgpt-paper-search","findings":[{"id":"cmuxiir850my7ad072zxpwkw7","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T08:43:40.578Z","lastVerifiedAt":"2026-10-22T08:43:40.578Z","lastChangeDetectedAt":"2026-10-06T05:57:24.249Z","scannedHash":"aa62a7ea06d15a37b3915027abcc8790fb89efc4","latestUpstreamHash":"aa62a7ea06d15a37b3915027abcc8790fb89efc4","nextCheckDueAt":"2026-10-23T06:38:51.146Z"}},{"id":"cmtw0nj40b9lcad07uabjjbh0","slug":"pdf","publicId":"2636ff7f-0fd3-4890-9118-62d6f7dddbb2","name":"pdf","description":"Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.","author":"","version":"1.2","license":"Proprietary. LICENSE.txt has complete terms","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:13.342Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pdf","findings":[{"id":"cmtw0nj41b9lead07bfmpksbd","source":"vettd","category":"structure","label":"scripts/ directory present","detail":"Bundled executable scripts found","severity":"info","ruleId":"VTD-0096"},{"id":"cmtw0nj41b9ljad0757r309u0","source":"vettd","category":"description","label":"Description within character limit","detail":"437/1024 characters used","severity":"info","ruleId":"VTD-0110"},{"id":"cmtw0nj41b9luad07sozp6u1i","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/extract_form_field_info.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9lyad07q0df3tig","source":"vettd","category":"security","label":"No secrets or unsafe code patterns detected","detail":"Scanned all files for credentials, private keys, and code-level risks (eval, shell exec, destructive ops)","severity":"info","ruleId":"VTD-0091"},{"id":"cmtw0nj41b9lzad07l6krbssy","source":"vettd","category":"security","label":"No prompt injection or jailbreak signals detected","detail":"Scanned text content for instruction override, jailbreak framing, credential solicitation, and embedded injection markers","severity":"info","ruleId":"VTD-0092"},{"id":"cmtw0nj41b9lqad07t66y7t8p","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/check_bounding_boxes.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9lxad07de7m9uhq","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/fill_pdf_form_with_annotations.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9lkad078ei9j6nb","source":"vettd","category":"description","label":"Description includes usage context","detail":"Good: description explains when to activate the skill","severity":"info","ruleId":"VTD-0111"},{"id":"cmtw0nj41b9lnad07q9yw90xk","source":"vettd","category":"best-practices","label":"Examples included","detail":"Found code blocks, input/output samples, or an examples section — concrete samples help agents pattern-match effectively","severity":"info","ruleId":"VTD-0103"},{"id":"cmtw0nj41b9liad07bpli49dc","source":"vettd","category":"security","label":"No repository link","detail":"No repository field found in SKILL.md frontmatter. Skills without a verifiable source repository cannot be externally audited.","severity":"info","ruleId":"VTD-0083"},{"id":"cmtw0nj41b9llad07zmnqjfcv","source":"vettd","category":"description","label":"Description overclaims scope","detail":"Broad trigger words (anything, everything, all files, etc.) widen attack surface — narrow to specific use cases","severity":"low","ruleId":"VTD-0113"},{"id":"cmtw0nj41b9lhad07lkdub5an","source":"vettd","category":"best-practices","label":"Skill name collides with well-known skill","detail":"\"pdf\" matches a well-known skill name — may cause unintended invocation","severity":"medium","ruleId":"VTD-0100"},{"id":"cmtw0nj41b9lmad07dgngztg6","source":"vettd","category":"best-practices","label":"SKILL.md body length is reasonable","detail":"313 lines (recommended: under 500)","severity":"info","ruleId":"VTD-0101"},{"id":"cmtw0nj41b9load07q15bsetq","source":"vettd","category":"best-practices","label":"No clear workflow structure","detail":"Consider adding numbered steps or a structured procedure for the agent to follow","severity":"info","ruleId":"VTD-0106"},{"id":"cmtw0nj41b9m0ad07kha66mag","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmtw0nj41b9lfad078ui79f3h","source":"vettd","category":"evals","label":"No evaluation test cases","detail":"Add an evals/ directory with test prompts and expected outputs to measure skill quality","severity":"info","ruleId":"VTD-0118"},{"id":"cmtw0nj41b9lsad07dfza0hwb","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/convert_pdf_to_images.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9ldad07mg2c31dj","source":"vettd","category":"structure","label":"SKILL.md present","detail":"Required skill definition file found","severity":"info","ruleId":"VTD-0095"},{"id":"cmtw0nj41b9lpad07tb1ezrlj","source":"vettd","category":"best-practices","label":"Progressive disclosure used","detail":"SKILL.md body references files in references/, scripts/, or assets/ — agents can load additional context on demand instead of consuming everything upfront","severity":"info","ruleId":"VTD-0107"},{"id":"cmtw0nj41b9lwad07s2c7k4ad","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/fill_fillable_fields.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9lgad0799hxmn82","source":"vettd","category":"structure","label":"Valid name field","detail":"Name \"pdf\" follows spec (lowercase, hyphens, ≤64 chars)","severity":"info","ruleId":"VTD-0099"},{"id":"cmtw0nj41b9lrad07fnx61coa","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/check_fillable_fields.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9ltad07ehj9trvg","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/create_validation_image.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0nj41b9lvad07dq6y9o67","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/extract_form_structure.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"unreachable","reason":"ref_not_found","retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-16T09:32:41.441Z","lastVerifiedAt":"2026-09-30T09:29:06.533Z","lastChangeDetectedAt":"2026-10-01T08:29:55.166Z","scannedHash":"808f38c0137805091270b6aa34c68aa92f254963","latestUpstreamHash":"b59da9d43562ef59d7ea682f9e4509df2dc08355","nextCheckDueAt":"2026-10-23T09:32:41.441Z"}},{"id":"cmuxinz3l0tljad07nn1z6m1i","slug":"benchling-integration","publicId":"a119438e-3b10-42fa-a04e-30c35bb6faa4","name":"benchling-integration","description":"Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.","author":"","version":"","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:12.128Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/benchling-integration","findings":[{"id":"cmuxinz3l0tlkad07tmzyshbw","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T05:17:39.957Z","lastVerifiedAt":"2026-10-22T05:17:39.957Z","lastChangeDetectedAt":"2026-10-06T09:30:24.284Z","scannedHash":"10ca4f6f7dcf28fcb54967dc63a7f545500f998d","latestUpstreamHash":"10ca4f6f7dcf28fcb54967dc63a7f545500f998d","nextCheckDueAt":"2026-10-23T07:20:03.628Z"}},{"id":"cmuxipg9p0w1vad07wqac4gva","slug":"pyzotero","publicId":"abfcc896-0038-4226-ac9a-5552026fa428","name":"pyzotero","description":">-","author":"","version":"","license":"MIT License","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:09.537Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pyzotero","findings":[{"id":"cmuxipg9p0w1wad07gnhdgq5j","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T12:04:42.808Z","lastVerifiedAt":"2026-10-22T12:04:42.808Z","lastChangeDetectedAt":"2026-10-06T11:26:24.309Z","scannedHash":"08c3fdc15be293b5643f94bac18a5f2ecec09d37","latestUpstreamHash":"08c3fdc15be293b5643f94bac18a5f2ecec09d37","nextCheckDueAt":"2026-10-23T13:06:25.514Z"}},{"id":"cmtw0ng60b9ijad07dfkgcn35","slug":"docx","publicId":"02043832-6bbe-4d09-aa1f-e0b593ff32bb","name":"docx","description":"Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation.","author":"","version":"2.1","license":"Proprietary. LICENSE.txt has complete terms","overallGrade":"C","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:09.525Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/docx","findings":[{"id":"cmtw0ng60b9j2ad078zcq1zi8","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/office/validators/pptx.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9iyad070c4v2ftf","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/merge_runs.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9ilad07mqnpyu0t","source":"vettd","category":"structure","label":"scripts/ directory present","detail":"Bundled executable scripts found","severity":"info","ruleId":"VTD-0096"},{"id":"cmtw0ng60b9j5ad071iq6w9q3","source":"vettd","category":"security","label":"No prompt injection or jailbreak signals detected","detail":"Scanned text content for instruction override, jailbreak framing, credential solicitation, and embedded injection markers","severity":"info","ruleId":"VTD-0092"},{"id":"cmtw0ng60b9izad07meu54ot3","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/office/soffice.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9j1ad07meimdj4g","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/office/validators/docx.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9j8ad0739d4kbiz","source":"cisco","category":"security","label":"Archive extraction followed by execution","detail":"SKILL.md:55 — An archive is extracted and its contents are then executed. This pattern can deliver and run malicious payloads hidden in archives.","severity":"high","ruleId":"COMPOUND_EXTRACT_EXECUTE"},{"id":"cmtw0ng60b9ikad07lp04km0h","source":"vettd","category":"structure","label":"SKILL.md present","detail":"Required skill definition file found","severity":"info","ruleId":"VTD-0095"},{"id":"cmtw0ng60b9inad07ilol7cxk","source":"vettd","category":"structure","label":"Valid name field","detail":"Name \"docx\" follows spec (lowercase, hyphens, ≤64 chars)","severity":"info","ruleId":"VTD-0099"},{"id":"cmtw0ng60b9itad07if9a21gy","source":"vettd","category":"best-practices","label":"No clear workflow structure","detail":"Consider adding numbered steps or a structured procedure for the agent to follow","severity":"info","ruleId":"VTD-0106"},{"id":"cmtw0ng60b9isad07cw6plz6n","source":"vettd","category":"best-practices","label":"Examples included","detail":"Found code blocks, input/output samples, or an examples section — concrete samples help agents pattern-match effectively","severity":"info","ruleId":"VTD-0103"},{"id":"cmtw0ng60b9iuad07gew1dytx","source":"vettd","category":"best-practices","label":"Validation loop referenced","detail":"Instructions for the agent to validate its own work before proceeding","severity":"info","ruleId":"VTD-0105"},{"id":"cmtw0ng60b9ixad07iomg019e","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/comment.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9j6ad07v901mh0n","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmtw0ng61b9j9ad07f216odnd","source":"cisco","category":"security","label":"CODE EXECUTION detected by YARA","detail":"scripts/accept_changes.py:99 — Detects dangerous code execution patterns with untrusted input in agent skills: subprocess.run(\n            [\n                \"soffice\",\n                \"--headless\",","severity":"medium","ruleId":"YARA_code_execution_generic"},{"id":"cmtw0ng60b9ivad07t2as7ofn","source":"vettd","category":"best-practices","label":"Progressive disclosure used","detail":"SKILL.md body references files in references/, scripts/, or assets/ — agents can load additional context on demand instead of consuming everything upfront","severity":"info","ruleId":"VTD-0107"},{"id":"cmtw0ng60b9j0ad07nu3e54iy","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/office/validate.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9imad075vc0eab7","source":"vettd","category":"evals","label":"No evaluation test cases","detail":"Add an evals/ directory with test prompts and expected outputs to measure skill quality","severity":"info","ruleId":"VTD-0118"},{"id":"cmtw0ng60b9j4ad075xymwlfz","source":"vettd","category":"security","label":"No secrets or unsafe code patterns detected","detail":"Scanned all files for credentials, private keys, and code-level risks (eval, shell exec, destructive ops)","severity":"info","ruleId":"VTD-0091"},{"id":"cmtw0ng60b9irad076j1uh1t3","source":"vettd","category":"best-practices","label":"SKILL.md body length is reasonable","detail":"90 lines (recommended: under 500)","severity":"info","ruleId":"VTD-0101"},{"id":"cmtw0ng60b9j3ad073054irhg","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/office/validators/redlining.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9ioad07k5c9z6j4","source":"vettd","category":"security","label":"No repository link","detail":"No repository field found in SKILL.md frontmatter. Skills without a verifiable source repository cannot be externally audited.","severity":"info","ruleId":"VTD-0083"},{"id":"cmtw0ng60b9iwad07gpolagr0","source":"vettd","category":"scripts","label":"CLI help supported","detail":"scripts/accept_changes.py: Script documents its interface via --help or argument parsing","severity":"info","ruleId":"VTD-0114"},{"id":"cmtw0ng60b9iqad077zu1v6gn","source":"vettd","category":"description","label":"Description includes usage context","detail":"Good: description explains when to activate the skill","severity":"info","ruleId":"VTD-0111"},{"id":"cmtw0ng60b9ipad07tfq8lrux","source":"vettd","category":"description","label":"Description within character limit","detail":"835/1024 characters used","severity":"info","ruleId":"VTD-0110"},{"id":"cmtw0ng60b9j7ad07hcwby945","source":"cisco","category":"security","label":"Archive extraction followed by execution","detail":"SKILL.md:45 — An archive is extracted and its contents are then executed. This pattern can deliver and run malicious payloads hidden in archives.","severity":"high","ruleId":"COMPOUND_EXTRACT_EXECUTE"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"C","criticalCount":0,"highCount":2}],"freshness":{"status":"unreachable","reason":"ref_not_found","retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-16T09:17:41.425Z","lastVerifiedAt":"2026-09-30T08:42:06.455Z","lastChangeDetectedAt":"2026-10-01T09:46:55.238Z","scannedHash":"78a36e2334e2224f28c07eed5ab8988c56f7ec4c","latestUpstreamHash":"4d53ad8037fd930066381405fe79a7235b7aafed","nextCheckDueAt":"2026-10-23T09:17:41.425Z"}},{"id":"cmuxit6ds10g9ad07htlh3blv","slug":"pi-agent","publicId":"beb58857-6f06-4098-b0ad-21ef68cc9ee0","name":"pi-agent","description":"Builds with and operates Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions, running local models through the llama.cpp router, developing custom Pi providers and TUI components, or using ecosystem packages such as pi-subagents (delegation/orchestration), pi-mcp-adapter (MCP servers), pi-interview (interactive forms), and pi-web-access (web search, fetching, video understanding).","author":"","version":"1.6","license":"MIT","overallGrade":"F","badgeStatus":"flagged","publishedAt":"2026-09-10T21:05:09.506Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pi-agent","findings":[{"id":"cmuxit6dt10gaad07msu250ol","source":"vettd","category":"security","label":"Embedded prompt-template marker","detail":"Detected in references/compaction.md:50 — ``serializeconversation()` renders messages as `[user]:`, `[assistant thinking]:`, `[assistant]:`, `[assistant tool calls`","severity":"medium","ruleId":"VTD-0075"},{"id":"cmuxit6dt10gbad07do5wq8lk","source":"vettd","category":"security","label":"Embedded prompt-template marker","detail":"Detected in references/pi-mcp-adapter.md:172 — `mcp prompt templates register as slash commands `/mcp__<server>__<prompt>`, refreshed on connect. arguments support posi`","severity":"medium","ruleId":"VTD-0075"},{"id":"cmuxit6dt10gcad07wywu0of9","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxit6dt10gdad075zkgou2i","source":"cisco","category":"security","label":"Dangerous data flow in command pipeline","detail":"references/overview.md:1 — Pipeline downloads data from the network and executes it: `curl -fsSL https://pi.dev/install.sh | sh`. This is a remote code execution pattern. (Note: found in documentation file - may be instructional rather than executable.)","severity":"low","ruleId":"PIPELINE_TAINT_FLOW"},{"id":"cmuxit6dt10gead07ai02dn36","source":"cisco","category":"security","label":"PROMPT INJECTION detected by YARA","detail":"references/sdk.md:138 — Generic prompt injection patterns: systemPromptOverride","severity":"critical","ruleId":"YARA_prompt_injection_generic"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"C","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"F","criticalCount":1,"highCount":1}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T02:36:39.510Z","lastVerifiedAt":"2026-10-22T02:36:39.510Z","lastChangeDetectedAt":"2026-10-07T01:09:15.849Z","scannedHash":"d58e366037de652756b9ca8159abdfa7b79e1486","latestUpstreamHash":"d58e366037de652756b9ca8159abdfa7b79e1486","nextCheckDueAt":"2026-10-23T04:04:34.694Z"}},{"id":"cmuxiisiy0n95ad07bfs3nbqv","slug":"ontology-term-resolution","publicId":"9fd8996a-8db1-4551-ab04-dd8494f3296c","name":"ontology-term-resolution","description":"Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP. Triggers include \"ontology term\", \"ontology ID\", \"CURIE\", \"controlled vocabulary\", \"UBERON\", \"CL:\", \"MONDO\", \"HPO\", \"EFO\", \"ChEBI\", \"NCBITaxon\", \"GO term\", \"PATO\", \"Zooma\", \"Bioregistry\", \"Identifiers.org\", \"Ontobee\", \"annotate this tissue/cell type/disease\", and any request to emit or verify an identifier shaped like PREFIX:0001234.","author":"","version":"1.4","license":"MIT","overallGrade":"C","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:06.407Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/ontology-term-resolution","findings":[{"id":"cmuxiisiy0n96ad07d4xi0yjn","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxiisiy0n97ad07wgglfc3d","source":"cisco","category":"security","label":"Code makes network requests","detail":"SKILL.md — Skill code makes network requests. 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Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.","author":"","version":"1.4","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:06.387Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/pacsomatic","findings":[{"id":"cmuxihm010li1ad073zfge7hg","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T15:24:30.072Z","lastVerifiedAt":"2026-10-22T15:24:30.072Z","lastChangeDetectedAt":"2026-10-06T03:37:24.223Z","scannedHash":"508cf74540a2dd397d1b01b7cde1042bbbb58d9d","latestUpstreamHash":"508cf74540a2dd397d1b01b7cde1042bbbb58d9d","nextCheckDueAt":"2026-10-23T16:58:28.922Z"}},{"id":"cmuxiqlrr0x7oad07gtswlf0h","slug":"pytorch-lightning","publicId":"4a656b6d-9a5a-4efc-8fb4-d21e7db6c27c","name":"pytorch-lightning","description":"Deep learning framework (PyTorch Lightning / lightning package). 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Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.","author":"","version":"1.7","license":"BSD-2-Clause license","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:04.331Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/gget","findings":[{"id":"cmuxij05v0nrbad07qngao7vb","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"},{"id":"cmuxij05v0nrcad07rnt9in52","source":"cisco","category":"security","label":"Code uses search/grep patterns but Grep tool not in allowed-tools","detail":"SKILL.md — Skill restricts tools to ['Read', 'Write', 'Edit', 'Bash'] but code uses regex search patterns","severity":"low","ruleId":"VTD-0087"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T20:33:01.039Z","lastVerifiedAt":"2026-10-22T20:33:01.039Z","lastChangeDetectedAt":"2026-10-06T05:29:24.241Z","scannedHash":"89f6dc784c8737bba3311ea6a2878cb668cb5b0c","latestUpstreamHash":"89f6dc784c8737bba3311ea6a2878cb668cb5b0c","nextCheckDueAt":"2026-10-23T19:50:14.789Z"}},{"id":"cmuxiqsy80xmfad070eenxb9j","slug":"usfiscaldata","publicId":"22bffbad-3d8d-4e2f-b0cc-0c5caaa308d0","name":"usfiscaldata","description":"Queries the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates, foreign exchange rates, savings bonds, or U.S. government revenue and spending statistics.","author":"","version":"1.5","license":"MIT","overallGrade":"B","badgeStatus":"conditional","publishedAt":"2026-09-10T21:05:04.329Z","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/usfiscaldata","findings":[{"id":"cmuxiqsy80xmgad07zx38uzyi","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088"}],"scannerRuns":[{"source":"vettd","status":"success","verdict":null,"grade":"B","criticalCount":0,"highCount":0},{"source":"cisco","status":"success","verdict":null,"grade":"A","criticalCount":0,"highCount":0}],"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T10:12:40.704Z","lastVerifiedAt":"2026-10-22T10:12:40.704Z","lastChangeDetectedAt":"2026-10-08T08:29:35.569Z","scannedHash":"466650dd78b9b3810f4d57b60f8b5e5f202256e7","latestUpstreamHash":"466650dd78b9b3810f4d57b60f8b5e5f202256e7","nextCheckDueAt":"2026-10-23T08:01:39.563Z"}},{"id":"cmuxitf0l1125ad070idaevrz","slug":"datamol","publicId":"ecfd4d1e-cb7a-4299-b7d5-6f09e359ab9c","name":"datamol","description":"Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. 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