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概要と使いどころ
Creates and inspects Fabric Activator (Reflex) alerts: rules, their data sources, conditions, and the Teams or email action they fire, plus decoding an existing ReflexEntities definition. Choose it whenever someone wants to be told, or something done, when values cross a threshold. The pipeline delivering those values is eventstream-cli.
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Use the skill to control and verify the code interface configuration of your model — how Simulink® model elements are represented in the generated C or C++ code. This includes — (1) specifying names, types (storage classes), and placement of variables that represent model elements (for example, making a model parameter tunable as a global extern variable); (2) specifying names, types, and placement of functions that represent model algorithms; (3) selecting the deployment type (Component, Subcomponent, or Automatic); (4) selecting the interface configuration type (data or service interface); (5) linking a shared Embedded Coder dictionary to a model; (6) creating Embedded Coder dictionary entries and setting their properties; (7) for service interface configuration — specifying service interface definitions, including sender, receiver, client, and server services. Items 1 and 2 can be set per element or as a category-wide default. Item 1 applies to GRT and ERT models; the rest to ERT models only.
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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.
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Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitoring, treating MRD as a binary integrated detection call across the patient's full variant set (with a defined LoD95 and per-sample specificity) rather than a per-timepoint VAF threshold, and handling undetectable samples as left-censored at the per-sample limit of detection rather than true zeros. Covers tumor-informed bespoke vs tumor-naive design, landmark vs surveillance sampling, molecular-response definitions and their non-standardization, censoring-aware clearance kinetics, and the multiple-testing structure of repeated surveillance. Use when monitoring ctDNA during therapy, calling molecular relapse before imaging, or estimating clearance half-life from serial samples.
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Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs; MRSA <=15; C. difficile <=2; Klebsiella <=21), models within-host diversity and transmission bottlenecks, integrates contact-tracing data, distinguishes generation from serial interval, and attributes source via Bayesian source attribution (islandR). Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after a dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB or chronic HIV.
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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.
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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.
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Assigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR/SeqSero2 Salmonella, SerotypeFinder E. coli, Kaptive Klebsiella, SeroBA pneumococcus, spa+SCCmec S. aureus), and lineage callers (TB-Profiler/Mykrobe barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use when typing bacterial isolates for surveillance or outbreak investigation, choosing between cgMLST allele distance and core-SNP distance for cluster definition, harmonising calls across schemas/database versions, assigning MTBC lineage with the Napier 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with pangolin-data version pinning, or selecting a typing resolution to match the surveillance question.
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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.
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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.
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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.
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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.
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Capture and review Agent Skill observations, and create, run, diagnose, or iteratively improve Skill evaluations (evals) with the skill-up CLI. Use when the user asks to record explicitly attributed Skill usage or feedback; review observations or user-supplied traces/transcripts; turn an approved observation into a regression case; evaluate, test, regress, verify, fix, improve, iterate, or evolve a Skill; add or strengthen eval cases; write eval.yaml/case.yaml; run skill-up run/validate/list-cases/report/import/init; or migrate from Anthropic evals.json. Plugin observation capture/review require either the Codex skill-up plugin or an observer-enabled DSH skill-up plugin. User-supplied external evidence can be reviewed without a plugin; evaluation remains multi-engine.
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Implement Swift Codable models for JSON and property-list encoding and decoding with JSONDecoder, JSONEncoder, CodingKeys, and custom init(from:) or encode(to:). Use when parsing API responses, remapping keys, flattening nested JSON, handling date or data decoding strategies, decoding heterogeneous arrays, or integrating Codable with URLSession, SwiftData, or UserDefaults.
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Support automatic audio switching for paired third-party Bluetooth headphones or earbuds with AudioAccessoryKit. Use when a companion app registers an audio accessory, an app extension reports worn/removed placement or connected source-device changes, or AccessoryControlDevice capabilities and errors need handling. Do not use for general AVAudioSession routing, Bluetooth transport, or initial accessory pairing.
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Design, validate, and plan a startup from scratch. Covers market research, competitive analysis, business model, brand identity, product definition, financial projections, and validation experiments. Trigger when the user has a startup idea to explore, wants to validate a business concept, needs a business plan or lean canvas, asks for market sizing or competitive landscape, wants brand positioning or go-to-market strategy, or says anything like "I have an idea for..." or "is this idea worth pursuing". Also handles resuming from a previous checkpoint.
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This skill should be used when user asks to "use supabase CLI", "supabase init", "supabase start", "run migrations", "deploy edge functions", "manage Supabase project", or works with the supabase command-line tool for local development and project management.
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Build and validate experimental WebMCP tools for an existing web page. Use when an agent needs to expose a site's real workflows as page tools, create webmcp.init.js, define deterministic checks, or compare WebMCP with accessibility-tree automation.
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Microstrip, stripline, CPW, differential pairs, and crosstalk analysis for impedance-controlled PCB interconnects. TRIGGER: user asks to design or analyze a transmission line (microstrip, stripline, CPW, coplanar, differential pair), extract RLGC or per-unit-length parameters, compute trace impedance, analyze a PCB trace cross-section, or perform crosstalk/coupling analysis. Invoke BEFORE writing code — preferred over RF Toolbox analytical functions (txlineMicrostrip, txlineStripline, txlineCPW). SKIP: EM simulation/S-parameter extraction of an existing component (use matlab-analyze-em), material/stackup definition only (use matlab-manage-pcb-material), building custom non-catalog geometry (use matlab-assemble-pcb-layout), optimization sweeps (use matlab-optimize-pcb-design).
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Model, simulate, and optimize Serializer/Deserializer (SerDes) systems — serial and parallel links — using MATLAB SerDes Toolbox. Design NRZ and PAM-N links (PAM3 through PAM16) — explore equalization architectures (FFE, CTLE, DFE), sweep or optimize parameters with genetic algorithms, and characterize channels from loss models, S-parameter files, or crosstalk scenarios. Process captured waveforms through equalization chains, build eye diagrams, and decompose jitter. Deliver IBIS-AMI models for Tx, Rx, Redriver, or Retimer by exporting to Simulink and compiling .ami/.ibs/.dll/.so files. Covers the full arc from initial design exploration and parameter optimization to compliance testing and compiled model validation, including custom datapath blocks for nonstandard equalization.
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Import Gerber, ODB++, Allegro .brd, .mcm files for PCB boards and IC packages. Inspect nets, layers, shapes, and stackups. TRIGGER: user asks to import, read, or open a PCB layout file. Gerber files use gerberRead or PCBReader; ODB++, Allegro .brd, .mcm, and native formats use pcbFileRead. Also when inspecting nets, layers, components, or stackups from an imported board. Invoke BEFORE writing import code — the query API (cadnet, cadnetList, componentList) is specialized. SKIP: EM analysis or S-parameter extraction (use matlab-analyze-em), PDN/IR-drop analysis (use matlab-analyze-pcb-pdn), building custom geometry (use matlab-assemble-pcb-layout), material/stackup definition only (use matlab-manage-pcb-material).
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Turn raw MATLAB code into a published .mltbx toolbox — full pipeline from scope definition through packaging and release. Drives 8 phases with human checkpoints, enforcing ordering and dependencies. Use when asked to package, create a toolbox, or run the files-to-package pipeline.
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Build custom PCB structures with pcbComponent, shapes, Boolean ops, feeds, and multi-layer stackups for non-catalog geometries. TRIGGER: user asks to build, modify, or customize a pcbComponent — add/remove shapes, edit polygons, place feeds, add metal layers, cut slots, or create non-catalog RF structures. Also when modifying geometry of an existing catalog-designed component (e.g., adding pads, removing elements, editing vertices). Invoke BEFORE writing pcbComponent code — layer/shape/feed API is non-obvious. SKIP: designing catalog components like filters/couplers/txlines (use the specific matlab-design-pcb-* skill), material/stackup definition only (use matlab-manage-pcb-material), EM analysis (use matlab-analyze-em), importing PCB files (use matlab-read-pcb-layout).
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Foundation skill for all RoadRunner workflows: MATLAB path setup, connection, project/scene/scenario lifecycle, world settings, handle management, status, and close. Use when connecting to RoadRunner, managing projects/scenes/scenarios, setting world origin, checking status, closing RoadRunner, or when any downstream RoadRunner skill needs initialization.
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。