「provenance」の検索結果

Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths. Use for PrimeKG reproducibility, biological association lookup, and hypothesis generation with relation and data provenance preserved.

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Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic classifiers.

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Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.

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Drafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission preparation when scientific accuracy and traceability matter.

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Creates and audits editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Used when the requested deliverable is a PowerPoint research/conference poster and exact physical, printer, accessibility, provenance, and package-security checks are required.

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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.

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Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measured cycling data. Use for SPM or DFN electrochemical battery modeling, C-rate protocols, voltage cutoffs, parameter studies and numerical validation of battery simulations.

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Searches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results with reproducible provenance. Covers PubMed, PMC, Europe PMC, bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall, OpenCitations, PubTator3, Zenodo, Figshare, ROR, BioStudies, and DOAJ. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, biomedical entity annotations, deposited records (Zenodo, Figshare, BioStudies), institution ROR IDs, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".

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Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or mechanism-specific ignition-delay comparisons.

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Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. 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.

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Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance. Use for literature reviews, evidence synthesis, and finding experimental details beyond abstracts.

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Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run. Use when cloning or fetching data from OpenNeuro, DANDI, datasets.datalad.org, or any DataLad dataset; when a file in a dataset reads as a broken symlink or a small pointer instead of real data; when an analysis needs a machine-readable record of how each output was produced so it can be re-executed; or when publishing a dataset to siblings such as a GitHub repository plus a storage remote. Also use to decide between DataLad and plain Git for a data-carrying repository.

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Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Used when a scientific agent must branch deterministically on resolved, ambiguous, not-found, invalid, unsupported, or unavailable variant outcomes; chain a resolved public variant into related literature or publication details; or preserve evidence provenance without accepting patient, phenotype, family, segregation, or private case data.

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Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, or other database-backed fact must be retrieved reproducibly from a named source rather than inferred from general knowledge.

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Capture and retrieve durable YYLO Ledger artifact Records with intentional profiles, payload modes, provenance, retention, and secret-safe immutable evidence.

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Internal downstream skill for ctf-sandbox-orchestrator. CTF-sandbox workflow for CI/CD, registry, dependency drift, artifact provenance, image build, release pipeline, and runtime consumer challenges. Use when the user asks to trace dependency drift, registry pulls, malicious packages, build or release tampering, CI execution, artifact signing, or which shipped artifact the runtime actually consumes. Use only after `$ctf-sandbox-orchestrator` has already established sandbox assumptions and routed here.

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Internal downstream skill for ctf-sandbox-orchestrator. CTF-sandbox workflow for AI-agent, prompt-injection, MCP or toolchain, cloud, container, CI/CD, and supply-chain challenges. Use when the user asks to analyze prompt-to-tool flows, retrieval poisoning, mounted secrets, deployment drift, runtime-vs-manifest mismatches, registry provenance, or CI-produced artifacts under sandbox assumptions. Use only after `$ctf-sandbox-orchestrator` has already established sandbox assumptions and routed here.

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Use for software supply-chain security assessment covering SBOM, SCA, CI/CD pipelines, container images, build integrity, dependency provenance, and vulnerability reachability.

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Use when maintaining a durable Markdown knowledge store that agents compile from sources, when every number or quote in a wiki page must trace back to an immutable source, or when compiled pages need cheap drift detection against the code they describe. Teaches the raw/wiki/archive layout, per-claim provenance links, and git fingerprints for zero-token staleness checks.

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Verify supply chain integrity for AI agent plugins, tools, and dependencies. Use this skill when: - Generating SHA-256 integrity manifests for agent plugins or tool packages - Verifying that installed plugins match their published manifests - Detecting tampered, modified, or untracked files in agent tool directories - Auditing dependency pinning and version policies for agent components - Building provenance chains for agent plugin promotion (dev → staging → production) - Any request like "verify plugin integrity", "generate manifest", "check supply chain", or "sign this plugin"

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Compile documents, notes, web content, transcripts, research materials, or code repositories into an evidence-grounded, visualization-ready knowledge graph with semantically typed entity nodes, statement-level provenance, and typed relationship edges. Use with ov compile to create or incrementally refresh `entities/*.md` node artifacts and a root `relations.jsonl` edge file for people, organizations, groups, animals, places, products, projects, systems, services, modules, datasets, standards, documents, events, and other identifiable things.

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Correlate Windows registry keys (USBSTOR, MountedDevices), Event Logs, and setupapi.dev.log to reconstruct USB device connection history, first/last-plugged timestamps, and drive letter mappings. Use when investigating removable media usage, tracking device provenance, or building a timeline for suspected data exfiltration.

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Chief Data Officer advisory for startups: AI training data rights and consent provenance, data product strategy (warehouse vs lakehouse vs mesh, build-vs-buy), B2B customer-data-as-asset valuation and M&A readiness, data team org evolution. Use when deciding whether to train models on customer data, choosing data architecture, valuing data for fundraising or M&A, sequencing data hires, or when user mentions CDO, chief data officer, data strategy, data mesh, lakehouse, training data, data product, data monetization, or customer data asset. NOT a tactical data engineering skill — strategic decisions only.

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Flag concrete false-positive proof introduced by changed specs, not test helper or channel preferences. Advisory only; never gates Warden clearance.

日本語の概要は準備中です。原文の説明を表示しています。