「structural」の検索結果

ALWAYS invoke this skill before asking the user any technical question or offering options, and whenever they ask to be asked in plain words - "ask simple", "ask me simply", "ask me in plain words" - in any language. ALWAYS invoke it too when the user asks for your view on a technical choice: whether it is worth doing, more than the problem needs, or replaceable by something simpler, and which option you would take. Invoke it even when the code makes the answer look obvious: the checks are what make the answer more than a guess. Rewrites the question in plain words and always ends with one marked recommendation. A structural choice first passes six checks, shown as a table: effort now, simpler substitute, extra work later, lock-in, over-engineering, easy to undo. Doing nothing is always weighed.

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Use when assembling the proof appendix and any code/data deposit for an American Economic Journal: Microeconomics (AEJ: Micro) manuscript under the AEA Data and Code Availability Policy. Covers proof appendices for pure theory plus numerical/structural/experimental code; it does not run your estimation.

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Use when the identification argument is the bottleneck for an American Economic Review: Insights (AER: Insights) short-format manuscript — causal identification in an empirical design, parameter identification in a structural model, or treatment-effect identification in an experiment. Stress-tests the strategy so it is clean enough to defend in a few pages, before exhibits are finalized.

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Use when the quantitative model is the bottleneck for an American Economic Journal: Macroeconomics (AEJ: Macro) manuscript — DSGE, New Keynesian, heterogeneous-agent (HANK / Aiyagari-Bewley), or structural estimation — and calibration, parameter identification, solution accuracy, or counterfactual validity need discipline. For empirical shock identification see aejmac-identification.

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Use when the question is what makes the result tight or what the data identify for an American Economic Journal: Microeconomics (AEJ: Micro) manuscript — covering both (a) structural/empirical-IO and experimental identification and (b) for pure theory, which assumptions drive the result and how robust the mechanism is. Stress-tests credibility; it does not build the model (see aejmic-theory-model).

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Use when a model — a full theory paper's argument or the structural/conceptual scaffolding behind an empirical AER: Insights short-format manuscript — needs to be made minimal, so it carries the single insight in a few pages. Keeps only what the insight requires; it does not develop a general framework.

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Use when an American Economic Journal: Applied Economics (AEJ: Applied) manuscript needs a model to interpret, discipline, or structure its empirical estimates — not to lead the paper. Calibrates how much theory belongs in an empirical-first journal and where it goes; it does not design the identification (aeja-identification) or build a standalone structural estimation.

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Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.

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Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.

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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

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Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks, multi-data tracks (scatter, histogram, heatmap), chord/link arcs for interactions, and explicit circos.clear() between plots. Covers when circular is appropriate vs when Cartesian wins (Cleveland-McGill 1984), karyograms, and chromosome adjacency in chord diagrams. Use when adjacency on the circle conveys meaning — chromosome-level overview, structural variants, Hi-C interactions, cross-genome comparisons.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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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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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Write and debug ast-grep rules for structural code search and rewrite. Use when tasks require AST-aware matching (not plain text), such as finding specific syntax shapes, relational patterns (inside/has), composite logic (all/any/not), or precise code refactors across a codebase.

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Edit Elementor pages and manage templates on WordPress sites via browser automation (for visual / structural changes) or WP-CLI (for safe text replacements). Use whenever the user wants to edit an Elementor page, update text in Elementor widgets, apply or manage Elementor templates, or make content changes to pages built with the Elementor page builder.

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Record a dated snapshot of the vault's health numbers and compare against previous snapshots so trends are visible. Use this skill for a monthly or quarterly check, when the user asks whether the vault is improving, or asks to track its numbers over time. Do NOT use for a one-off graph analysis, which is second-brain-graph, or for structural repairs.

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Produce a periodic review of a second-brain vault: what was added, which topics are growing, what contradicts what, which questions are still open, and what is worth reading next. Use this skill whenever the user asks for a weekly or monthly review, asks what changed in their vault, what they have been learning about lately, or what they should look at next, and when a scheduled review task fires. Do NOT use for structural linting, for ingesting sources, or for answering a specific factual question.

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Validate a third-party control repo across four automated layers plus one printed manual recipe. Layer 1 asserts native-source structure (Android getName() and iOS +moduleName to manifest nativeModule; @ReactMethod / RCT_EXPORT_METHOD to methods; no @ReactModule) plus load/init readiness (ReactPackage public no-arg constructor, iOS [cls new] no-arg init, requiresMainQueueSetup NO, non-throwing eager construction), so launch-time crashes surface before any build. Layer 2 validates the committed `./manifest.json` against the ppmplugin-format rules. Layer 3 asserts request/response/error-code agreement across native and PCF. Layer 4 compiles the PCF (auto-skipped if absent). Layer 5 prints a device end-to-end recipe. Native compile belongs to /build-android-binary and /build-ios-binary — this is the cheap structural pre-flight before those slow builds. Reports pass/fail per layer with a fix hint and updates .extension-state.md.

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