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概要と使いどころ
Tests Simulink models using either ephemeral Gherkin-based tests (model_test) for quick validation or persistent tests (Simulink Test API) authored from requirements or behavioral specs. Requires Simulink Test.
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Use when writing or editing Simscape Language (.ssc) source files — components, domains, or functions. Triggers include: model a physical component in .ssc; write physical equations for a Simscape block; add or modify physics or parameterization options in a Simscape component; build a composite component. Also use for validating .ssc syntax, fixing Simscape Language errors, or converting governing equations into working Simscape component code. Do NOT use for configuring or connecting existing Simscape blocks in a Simulink model — that is model building, not language authoring.
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Common steps for building multi-layer system architecture models using System Composer. Use when implementing architecture models or when interacting with interface dictionaries, allocation sets, stereotypes, and requirements for architecture components.
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Linearize Simulink models. Use when obtaining linear time invariant or linear parameter varying models from Simulink models.
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Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the somatic/trio/RNA boundary to the ClairS/Clair3-Trio family. Use when calling germline SNVs/indels from ONT or HiFi BAMs, choosing a Clair3 model, phasing variants, or benchmarking long-read calls.
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Predict B-cell and T-cell epitopes for vaccine antigen design and epitope mapping with BepiPred-3.0, DiscoTope-3.0, the IEDB tools, and EL-mode MHC presentation. Encodes the load-bearing asymmetry that T-cell epitope prediction is mature (it reduces to MHC presentation, AUC>0.9) while B-cell prediction is unreliable (linear predictors ~AUC 0.6 because ~90% of real epitopes are conformational) — so structure-based DiscoTope-3.0 on AlphaFold models is the only defensible B-cell path, propensity scales are obsolete, and NetChop is largely redundant on EL-trained models. Use when mapping epitopes or selecting vaccine antigens. MHC binding lives in mhc-binding-prediction.
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.
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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.
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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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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.
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Use when implementing, testing, or evaluating ANY Apple Intelligence, on-device AI, or speech-to-text feature. Covers Foundation Models, @Generable, LanguageModelSession, Tool protocol, eval suites, model-as-judge scoring, SpeechTranscriber, CoreML.
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Use when the user mentions Foundation Models review, on-device AI audit, LanguageModelSession issues, or @Generable/guardrail problems — including missing availability checks, manual JSON parsing, and guardrail handling.
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Use when the user wants to modernize iOS code to iOS 17/18 patterns, migrate from ObservableObject to @Observable, update @StateObject to @State, or adopt modern SwiftUI APIs.
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Apply modern Swift language patterns and idioms for non-concurrency, non-SwiftUI code. Covers if/switch expressions (Swift 5.9+), typed throws (Swift 6+), result builders, property wrappers, opaque and existential types (some vs any), guard patterns, Never type, Regex builders (Swift 5.7+), basic Codable shaping (CodingKeys, custom decoding, nested containers), modern collection APIs (count(where:), contains(where:), replacing()), basic FormatStyle usage, and string interpolation patterns. Use when writing core Swift code involving generics, protocols, enums, closures, or modern language features; route deep Codable to swift-codable, detailed formatting/localization to swift-formatstyle, and API naming to swift-api-design-guidelines.
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Implement computer vision features including text recognition (OCR), face detection, barcode scanning, image segmentation, object tracking, and document scanning in iOS apps. Covers both the modern Swift-native Vision API (iOS 18+) and legacy VNRequest patterns, VisionKit DataScannerViewController for live camera scanning, and CoreMLRequest/VNCoreMLRequest for custom model inference. Use when adding OCR, barcode scanning, face detection, or custom Core ML model inference with Vision.
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Build private, on-device AI features on iPhone, iPad, and Mac with Foundation Models, Core ML, MLX Swift, or llama.cpp. Use when choosing an Apple-local model runtime, building an Apple Intelligence chatbot or tool-calling feature, running an LLM on Apple Silicon, converting or compressing a Python model for Core ML, or comparing on-device inference backends. For Swift Core ML loading and prediction code, use the coreml skill.
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This skill should be used when user asks to "upload my model to Ultralytics Platform", "push this run to the platform", "upload a dataset to platform", "download a dataset from platform", "search platform datasets", "start cloud training", "train on platform GPUs", "export a model on platform", "deploy a model endpoint", "run Moondream on Platform", "auto-annotate a Platform dataset", "run hosted AI inference", "why is my run not showing on platform", or mentions platform.ultralytics.com, ul:// URIs, ultralytics-platform, or ULTRALYTICS_API_KEY.
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Discover OPC UA servers, connect MATLAB clients, and browse/navigate server nodes using opcuaserverinfo, the Local Discovery Service (LDS), opcua, connect, setSecurityModel, certificate-trust functions, findNodeById, opcuanode, and Namespace/Children traversal. Use when finding OPC UA servers on the network, querying endpoints and security policies, connecting to a server, authenticating with username/password or certificates, configuring security modes, handling certificate-trust or hostname-mismatch errors, troubleshooting failed connections or empty discovery, inspecting an OPC UA certificate (.der/.pem), browsing an address space, finding nodes by name or NodeId, navigating node hierarchies, invoking method nodes, or batch-processing large namespaces. Trigger on: opcuaserverinfo, LDS, opcua, opc.ua.Client, setSecurityModel, opc.ua.trustServerCertificate, OPC UA certificate, findNodeById, opcuanode, browse OPC UA, find node, OPC UA namespace, OPC UA method node, Industrial Communication Toolbox.
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Port MATLAB Data Acquisition Toolbox code from the discouraged (legacy) session-based interface (daq.createSession, addAnalogInputChannel, startBackground, DataAvailable listeners, queueOutputData, wait) to the recommended DataAcquisition interface (daq("ni"), addinput, start, ScansAvailableFcn, write, preload). Use when migrating legacy DAQ scripts, converting session-API calls, working with DataAcquisition objects, writing multi-feature DAQ scripts that combine triggers, callbacks, continuous acquisition, or analog output. Also use when a user says their DAQ script "used to work" or "errors on R20XX", since modernizing legacy session-API code is a frequent fix for those failures. Trigger keywords: daq, DAQ, NI, session interface, addtrigger, addclock, ScansAvailableFcn, ScansRequiredFcn, daq.createSession, addAnalogInputChannel, startBackground, queueOutputData, DataAvailable, evt.Data, evt.TimeStamps, wait(d), preload, discouraged, legacy, modernize, R2020a.
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Via modeling: pads, antipads, ground return vias, GRV placement, and signal integrity for high-speed layer transitions. TRIGGER: user asks to model a via, design a via transition, place ground return vias, analyze via performance, or check signal integrity through layer transitions. Invoke BEFORE writing code — only viaSingleEnded exists (no viaDifferential), and the location format is non-obvious. SKIP: general signal integrity without vias (use matlab-analyze-em), transmission line design (use matlab-design-pcb-transmission-line), PDN analysis (use matlab-analyze-pcb-pdn), material/stackup setup only (use matlab-manage-pcb-material).
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Style MATLAB charts and figures. colororder palettes for chart series colors, colormap selection, brand color organization, and the R2025a Theme API for uifigure apps (dark mode with fliplightness, ThemeChangedFcn, uistyle, component colors). Use when customizing chart colors, applying a color palette, organizing brand colors, implementing dark mode, or importing an external color scheme. Triggers: theme, dark mode, brand colors, colororder, colormap, palette, fliplightness, color scheme, styling, chart colors.
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Build, modify, and diagram SimBiology models — API reference, helper functions, and layout patterns. Use when constructing or editing models programmatically or visually.
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