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Europe PMC RESTful Web Service 多源文献聚合检索原子 skill。一次调用同时召回 PubMed + PMC + AGRICOLA + CABI + 预印本(bioRxiv / medRxiv / ChemRxiv 等)+ 灰色文献,自动按 PMID/PMCID/DOI 三级去重,返回完整元数据(含全文 OA 链接、citations metadata、grants 资助信息)。当任务出现 Europe PMC、多源文献聚合、广召回、RAG 检索、预印本搜索、bioRxiv、medRxiv、全文链接、DOI 检索、跨库去重、灰色文献、资助检索 等触发词时使用。**定位**:广召回 · 多源聚合 · RAG 友好(与 pubmed-eutils 互补——后者做精准官方源、Clinical Queries;本 skill 做"撒网"式广召回)。**不做**:NCBI E-utilities 直检(交给 pubmed-eutils)、临床试验(clinical-trials-v2)、全文 XML 抽取(bioc-fulltext-fetch)、实体识别(pubtator-entity-search)、证据分级(medical-evidence-grading)。

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给定 PMID / PMCID 取结构化全文（BioC XML/JSON）。封装 NLM BioC PubMed API（标题+摘要）和 BioC PMC OA API（开放获取全文），输出按章节切分的段落、表格上下文、RAG 友好 chunk。适合大批量入向量库。触发词：全文抽取 / BioC / RAG 入库 / 文献全文 / PMC 开放获取 / structured fulltext / 段落抽取 / 表格抽取 / fulltext to vector store。

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吉里吉里Z (kirikiri Z) 本体クラス API のリファレンス。TJS2 で吉里吉里Z 上のスクリプトを書く、レビューする、デバッグするときに使う。Layer / Window / Bitmap / System / Storages / Font / Plugins / Timer / Debug / AsyncTrigger / Scripts / BinaryStream / Matrix32 / Matrix44 / Rect / ImageFunction のコア API、サウンド系 (WaveSoundBuffer / SoundBuffer / VideoOverlay)、DrawDevice (BasicDrawDevice / SDLDrawDevice / OGLDrawDevice / GPUDrawDevice / NullDrawDevice)、OpenGL 描画系 (Canvas / Texture / ShaderProgram / Offscreen / VertexBinder / VertexBuffer)、および主要プラグイン提供クラス (HttpRequest / GdiPlus.* / WIN32Dialog / CSVParser / LineParser / Process / Pad / MenuItem / Unzip / Zip / PSD / SimpleHTTPServer) を網羅。**呼び出されたら必ず「共通パターン」と「クロスカッティング概念」を確認し、必要な詳細クラスは doc/reference/*.md を Read しに行くこと。** TJS2 言語そのものや組み込みクラス (Array / Dictionary / Math 等) は別 skill (`tjs2`) を参照。エンジン内部構造 (C++ 実装、レンダリングパイプライン詳細) は対象外。

Detects and analyzes malicious behavior in mobile applications through behavioral analysis, permission abuse detection, network traffic monitoring, and dynamic instrumentation. Use when analyzing suspicious mobile applications for data exfiltration, command-and-control communication, credential stealing, SMS interception, or other malware indicators. Activates for requests involving mobile malware analysis, app behavior monitoring, trojan detection, or suspicious app investigation.

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Knowledge base from NASA-STD-8729.1A — NASA's R&M (Reliability and Maintainability) standard covering spaceflight and support systems (Revision A, 2017-06-13). Use for NASA's objectives-driven R&M framework — the R&M objectives hierarchy (one Top Objective decomposed into four sub-objectives, paired with tailorable strategies), how R&M requirements are established inside the SMA Plan required by NPR 7120.5, the SMA Technical Authority concurrence/independent-evaluation governance, milestone vs. readiness review gates, the reliability/maintainability/availability vocabulary (Ai vs. Ao, the failure causal chain, risk as a triplet), and the R&M Evidentiary Methods catalogue (FMEA/FMECA, FTA, RBDA, RCM, LORA, plus the space-environment and parts-pedigree analyses). Scoped to NASA spaceflight and support systems and to assurance planning: it is an objectives-and-strategies standard, so it deliberately does NOT prescribe step-by-step analysis procedures (those live in the referenced NASA Preferred Reliability Practices) and is thin on facility R&M, detailed math/derivations, and non-NASA or commercial life cycles.

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Generate MSBuild binary logs (binlogs) for build diagnostics and analysis. Only activate in MSBuild/.NET build context. USE FOR: adding /bl:{} to any dotnet build, test, pack, publish, or restore command to capture a full build execution trace, prerequisite for binlog-failure-analysis and build-perf-diagnostics skills, enabling post-build investigation of errors or performance. Requires MSBuild 17.8+ / .NET 8 SDK+ for {} placeholder; PowerShell needs -bl:{{}}. DO NOT USE FOR: non-MSBuild build systems (npm, Maven, CMake), analyzing an existing binlog (use binlog-failure-analysis instead). INVOKES: shell commands (dotnet build /bl:{}).

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ペネトレーションテストを対話的に実行するスキル。認可確認(Authorization Gate)→カテゴリ選択（Methodology, Reconnaissance, Scanning, VulnerabilityScanning, WebAppTesting, APITesting, PasswordAttacks, Exploitation, PrivilegeEscalation, ActiveDirectory, PostExploitation, WirelessAttacks, NetworkAttacks, SocialEngineering, CloudPentesting, MobileAppTesting, ContainerK8s, BinaryExploitation, OWASPTop10, Reporting, EmailSecurity, DatabaseAttacks, VPNRemoteAccess の全23カテゴリ）→ツール選択→コマンド実行→発見記録(Finding)→レポート生成をステップバイステップで進行。スコープ/除外チェック・ガードレール付き。「ペンテスト実行」「pentest」「侵入テスト」「脆弱性診断」「セキュリティテスト」「pentest executor」で発火。

Detects and analyzes malicious behavior in mobile applications through behavioral analysis, permission abuse detection, network traffic monitoring, and dynamic instrumentation. Use when analyzing suspicious mobile applications for data exfiltration, command-and-control communication, credential stealing, SMS interception, or other malware indicators. Activates for requests involving mobile malware analysis, app behavior monitoring, trojan detection, or suspicious app investigation.

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End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition with MANDATORY PERMANOVA + PERMDISP pair (Anderson & Walsh 2013), constrained ordination, and the read-counts-not-abundance critique (Lamb 2019). Use when processing eDNA samples for biodiversity assessment, deciding ASV vs OTU, configuring OBITools3 v3, interpreting decontam screening, or reporting community comparisons with the dispersion confound check.

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Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Use this skill when adding a new symbiont (agent integration) to Myco's SymbiontInstaller — the component that manages agent lifecycle operations (init, update, remove, doctor) for all registered agents. Activates whenever you need to onboard a new AI agent (Claude Code, Cursor, Windsurf, a custom agent, etc.) so that `myco init`, `myco update`, and `myco doctor` manage its installation. Apply this skill even if the user doesn't explicitly mention SymbiontInstaller — any time you're adding a new agent type, creating a symbiont manifest, wiring new hook templates, or extending the supported agents list, this skill applies. Also relevant when a new symbiont needs the cross-platform hook guard or environment variable injection.

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Android Accessibility Service security analysis and pentesting. Use this skill whenever the user mentions Android security testing, accessibility service abuse, RAT detection, malware analysis, ClayRat, PlayPraetor, overlay phishing, credential harvesting, or any Android app security assessment involving AccessibilityService APIs. This skill helps detect malicious accessibility services, analyze abuse patterns, and harden apps against accessibility-based attacks.

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This skill should be used when the user asks for an accessibility review, accessibility audit, a11y check, WCAG compliance review, screen reader audit, "is this accessible?", "does my site meet WCAG?", "check my component for accessibility", "accessibility overview of this page", "review accessibility of", "check for a11y issues", "fix accessibility issues", or any request to audit a web page, component, or codebase for WCAG 2.2 AA compliance.

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.

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Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.

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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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