203 件 ・ 関連度順
概要と使いどころ
Map paper notes + taxonomy into a signal table of tensions, missing pieces, and promising academic axes for brainstorm discussion. Writes `output/trace/IDEA_SIGNAL_TABLE.md`.
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Build a retrieval-informed chapter skeleton (`outline/chapter_skeleton.yml`) from taxonomy/core scope before stable H3 decomposition.
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Audits existing tests in any language using formal, research-backed test smell names and the testsmells.org 19-smell academic taxonomy. Use when the caller asks for an academic or citable test-smell review, named smell categories, or a formal severity-ranked smell assessment. Covers Assertion Roulette, Conditional Test Logic, Mystery Guest, Eager Test, Sleepy Test, Unknown Test, Sensitive Equality, and the rest of the catalog across .NET, Python, JavaScript/TypeScript, Java, Go, Ruby, Rust, Swift, Kotlin, PowerShell, and C++. DO NOT USE FOR a quick pragmatic test review (use test-anti-patterns), writing or running tests, framework migration, coverage, or assertion-diversity metrics.
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Pseudo-mutation analysis ONLY: answer whether tests would catch a bug if production code changed, which meaningful changes would still pass, or which caller-visible mutations existing assertions would miss; verify candidates when requested, then optionally close verified gaps. Includes explicit read-only per-test composition for grading. Activate for behavioral blind spots tied to production behavior. Polyglot. DO NOT USE FOR: suite taxonomy, metadata, or distribution reports (test-tagging); .NET line-vs-branch or Cobertura interpretation, arithmetic, plateaus, project-wide coverage gaps, or coverage-backed test/CRAP priorities (coverage-analysis; use native coverage tooling outside .NET); named-target CRAP (crap-score); new suites (code-testing); assertion/smell audits; or mutation tools.
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Use when you need to apply Java exception handling best practices — including using specific exception types, managing resources with try-with-resources, securing exception messages, preserving error context via exception chaining, validating inputs early with fail-fast principles, handling thread interruption correctly, documenting exceptions with @throws, enforcing logging policy, translating exceptions at API boundaries, managing retries and idempotency, enforcing timeouts, attaching suppressed exceptions, and propagating failures in async/reactive code. This should trigger for requests such as Exception handling; Use try-with-resources in Java code; Create exception chaining in Java code; Apply fail-fast validation in Java code; Review Java exception taxonomy and propagation. Part of Plinth Toolkit
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ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
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ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.
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。
Estimate embodied carbon and produce ESG/climate reporting for construction: LCA per work item, material-based carbon factors, EU taxonomy and CSRD alignment. Use when a project needs carbon estimates or sustainability reporting.
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Material passports and circular construction: generate per-element material inventories from BOQ/BIM, mark reuse potential and recycled content, and prepare deconstruction data. Use for circular-economy and EU Taxonomy-aligned projects.
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CPU-only operating guidance for the BEHAVIOR-1K BDDL 3.7.0 package: symbolic activity definitions, condition parsing/evaluation, object taxonomy, and generated-data-backed knowledge-base inspection.
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Routes substantive ML, AI, data, scientific-computing, and software-engineering requests to the smallest useful set of managed repository skills. Invoke proactively when a request names or implies a package, framework, model family, dataset, modality, workflow, backend, deployment target, evaluation method, or implementation approach that may benefit from repository guidance, even if no repository is named. Narrow progressively from area to family to repository root: inspect only the one or two most likely area pages; compare candidates by capability, task surface, model/data format, training versus inference versus evaluation intent, runtime constraints, and root-skill description; then open only the selected root and relevant sub-skills, references, or scripts. Select multiple repositories only when each adds a distinct capability. Do not load the whole collection, treat dependencies or incidental integrations as capabilities, choose by name alone, or force a match when no exact taxonomy family applies.
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Provides a structured risk scoring methodology for Data Protection Impact Assessments aligned with ENISA threat taxonomy and ISO 29134. Covers likelihood and severity assessment, risk matrix construction, inherent vs residual risk calculation, and risk appetite thresholds per EDPB WP248rev.01 guidance. Keywords: risk scoring, DPIA risk matrix, likelihood, severity, ENISA, ISO 29134, residual risk, risk appetite.
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Implements technical breach detection capabilities including SIEM integration, DLP alert configuration, anomaly detection rules, and insider threat monitoring. Provides a breach classification taxonomy across confidentiality, integrity, and availability dimensions. Covers detection tool selection, alert tuning, and integration with privacy incident response workflows. Keywords: breach detection, SIEM, DLP, anomaly detection, insider threat, classification.
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Pre-publish assistant for new blog posts. Use when the user wants to classify a new post with categories and tags, generate SEO metadata (title, description, focus keyphrase), or get intelligent suggestions with rationale. Works with draft content (file path, URL, or text) and suggests from existing taxonomy to maintain balanced distribution.
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Think and work like an expert Microbial Physiologist. Use when a task calls for Microbial Physiologist judgment. Reasons from Monod/chemostat (μ = D), YX/S and Pirt maintenance, Crabtree/overflow, 13C-MFA and FBA, and BMSAB taxonomy; treats OD-as-biomass yield error, FBA-as-measured-flux, washout misread, and portable ms across media as first-class failure modes.
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Think and work like an expert Mammalogist. Use when a task calls for Mammalogist judgment. Reasons from mammalian life history and detectability-limited sampling through ASM MDD taxonomy, Sherman/camera-trap/SCR survey design, occupancy and SECR models, bat acoustic validation, and museum voucher discipline while treating trap heterogeneity, camera autocorrelation, closure violation, and WNS decontamination gaps as first-class failure modes.
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。
Think and work like an expert Environmental Microbiologist. Use when a task calls for Environmental Microbiologist judgment. Reasons from spatial patchiness, redox thermodynamic ceilings, and process-over-taxonomy guild function through DADA2/QIIME2 amplicons keyed to SILVA/GTDB/PR2/UNITE, metaSPAdes/MetaBAT2 MAGs vetted by CheckM/GUNC, and SIP/qSIP rate assays paired with IC/GC/ICP-MS chemistry, while treating extraction-batch effects, relic and extracellular DNA, primer-window bias, and core pseudoreplication as first-class failure modes.
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Think and work like an expert Cosmochemist. Use when a task calls for Cosmochemist judgment. Reasons from oxygen three-isotope taxonomy (Δ17O), chondrite–achondrite classification, and presolar grain NanoSIMS through Meteoritical Bulletin curation, Al–Mg and Pb–Pb isochrons, CRE vs formation-age separation, and clean-lab sample prep while treating terrestrial weathering, mount contamination, and breccia mixing as first-class failure modes.
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Think and work like an expert AI Researcher. Use when a task calls for AI Researcher judgment. Reasons from data generating processes, inductive biases, and compute-data-algorithm trade-offs through train/val/test discipline, seed sweeps, ablation ladders, and standards like NeurIPS reproducibility checklists, model cards, and lm-eval-harness, while treating data leakage (Kapoor & Narayanan taxonomy), benchmark contamination, spurious correlations, and reward-model overoptimization as first-class failure modes.
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End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal, denoising with OBITools3 or DADA2, contamination filtering, taxonomy assignment, Hill number diversity, and constrained ordination. Use when processing environmental DNA samples for biodiversity assessment or ecological surveys.
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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.
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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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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
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。
Workflow for amplicon microbiome analysis including denoising, taxonomy assignment, diversity analysis, and differential abundance.
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。