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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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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.

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。

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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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.

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.

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。

Provides expert knowledge of the testing pyramid, test design principles, MockK patterns, and integration testing conventions for Spring Boot + Kotlin projects.

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。

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.

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。

Performs simple mutation testing to verify test coverage and assertions.

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。

Audits Tailwind CSS usage ensuring mobile-first responsive utilities and clean classes.

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。

Guides the creation of complete Spring Boot features following a structured, layer-by-layer workflow: entity, repository, service, controller, and tests. Applies Kotlin idioms, Bean Validation, and MockK test patterns throughout.

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。

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。

Provides expert knowledge of the testing pyramid, test design principles, MockK patterns, and integration testing conventions for Spring Boot + Kotlin projects.

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 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。

Query and interpret security logs you are authorized to read. Build detections and investigations without leaking PII.

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。

Web Performance Engineering — analyzes Core Web Vitals using the PageSpeed Insights API (PSI v5) and applies the 80/20 principle: identify the 20% of changes that produce 80% of the performance gain. Produces a prioritized markdown report with quantified estimates and framework-specific code. Trigger: When auditing page speed, analyzing Core Web Vitals, or optimizing web performance for any URL.

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。

Build and configure Laravel 10+ applications, including creating Eloquent models and relationships, implementing Sanctum authentication, configuring Horizon queues, designing RESTful APIs with API resources, and building reactive interfaces with Livewire. Use when creating Laravel models, setting up queue workers, implementing Sanctum auth flows, building Livewire components, optimising Eloquent queries, or writing Pest/PHPUnit tests for Laravel features.

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。

Plan and report authorized vulnerability assessments on owned systems. Prioritize evidence, severity, and remediations. Do not deliver exploit payloads.

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。

Audit web pages for performance optimization following PageSpeed Insights guidelines. Use when analyzing page performance, optimizing web applications, reviewing performance metrics, implementing Core Web Vitals improvements, or when the user mentions page speed, performance optimization, Lighthouse scores, or Core Web Vitals.

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。

Automate detection, enrichment, and response playbooks for a SOC you operate. Keep humans in the loop for destructive actions.

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。

Audits Hibernate database interactions to prevent N+1 query problems in JVM apps.

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。

Advise on defensive security for industrial control systems you operate. Safety first. No process-disruption guidance.

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。

Harden iOS/Android apps you ship: storage, TLS pinning policy, IPC, and backend trust. You still enforce authz on the server.

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。