テスト・セキュリティのスキル

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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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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Track and report progress of a request to create and run an EcoSIM case for a site ("create an ecosim run for site US-UMB", "set up and run EcoSIM at <site>"). Records four stages — data preparation, namelist creation, model simulation, and output evaluation — in result/<SITE_ID>/progress.json and PROGRESS.md, derives step status from files and quality reports on disk, and records manual results such as the executable, test run, and evaluation verdicts. Use at the start of such a request, after each stage, and whenever the user asks where a site run stands.

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Generate a structured test plan for a feature or module — covers unit, integration, contract, and edge cases without writing implementation code.

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。

Spring Security best practices for authn/authz, validation, CSRF, secrets, headers, rate limiting, and dependency security in Java Spring Boot services.

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Provides JWT authentication and authorization patterns for Spring Boot 3.5.x covering token generation with JJWT, Bearer/cookie authentication, database/OAuth2 integration, and RBAC/permission-based access control using Spring Security 6.x. Use when implementing authentication or authorization in Spring Boot applications.

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Provides comprehensive testing patterns for Spring Boot applications covering unit, integration, slice, and container-based testing with JUnit 5, Mockito, Testcontainers, and performance optimization. Use when writing tests, @Test methods, @MockBean mocks, or implementing test suites for Spring Boot applications.

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。

Run the authorized defensive security workflow — domain security-* skills, authorization gate, risk-based routing, hardening, and review.

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。

Verification loop for Spring Boot projects: build, static analysis, tests with coverage, security scans, and diff review before release or PR.

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。

JPA/Hibernate patterns for entity design, relationships, query optimization, transactions, auditing, indexing, pagination, and pooling in Spring Boot.

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Generates Spring Boot 3.x configurations, creates REST controllers, implements Spring Security 6 authentication flows, sets up Spring Data JPA repositories, and configures reactive WebFlux endpoints. Use when building Spring Boot 3.x applications, microservices, or reactive Java applications; invoke for Spring Data JPA, Spring Security 6, WebFlux, Spring Cloud integration, Java REST API design, or Microservices Java architecture.

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。

Generate a structured test plan for a feature or module — covers unit, integration, contract, and edge cases without writing any implementation code.

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。

Run the PageSpeed performance audit — 80/20 analysis of Core Web Vitals using the PageSpeed Insights API.

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。

Run the bug fix workflow — risk-based routing through task validation, implementation, testing, and optional review.

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。

Run a structured Red-Green-Refactor TDD cycle — write a failing test first, implement the minimum code to pass it, then refactor with the suite green.

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。

Run the full feature workflow — task validation, technical design, implementation, testing, review, and documentation.

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Audita calidad de código Kotlin/Spring Boot en este proyecto. Úsalo cuando el usuario pida revisar código, verificar estándares, hacer un code review, auditar calidad, ejecutar linters, verificar cobertura, o antes de hacer commit/PR. También úsalo cuando mencionen KTLint, Detekt, JaCoCo, cobertura, o simplemente digan "revisa el código" / "está listo para commit" / "qué tan bueno está el código".

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Provides expert knowledge for implementing and reviewing application security following OWASP Top 10 (2021), with stack-specific patterns for Spring Boot, Django, Next.js, and Astro.

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Use when implementing authentication, authorization, JWT tokens, security filters, password encoding, or any Spring Security configuration. Covers stateless JWT auth, token rotation, RBAC, and method-level security.

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Use when writing tests of any kind — unit, slice, or integration. Covers test structure, naming conventions, Mockito patterns, @WebMvcTest, @DataJpaTest, and Testcontainers setup.

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Guides agents through Red-Green-Refactor with runner-captured evidence. Use when running /cc-tdd-cycle, writing tests before implementation, or Global TDD required is yes.

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。