574건 · 관련도순
Modify NVIDIA cuOpt itself, covering C++/CUDA solver code, Python bindings, server endpoints, and CI. Follow project conventions for environment setup, builds, tests, debugging, and contributions, including the required sign-off for submitted changes.
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Predict biomolecular structures and estimate how strongly a ligand binds using Boltz2 NIM. Submit proteins, DNA, RNA, and ligand inputs through NVIDIA's hosted API or local Docker, then save structures and inspect confidence and affinity scores.
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Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.
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Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
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DNS rebinding attack playbook. Use when testing applications that trust DNS resolution for origin checks, interact with internal services from browser context, or when SSRF is not possible server-side but the target has client-side fetch/XHR to attacker-controlled domains.
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Set up player input in Unreal Engine 5 with Enhanced Input: Input Actions, Input Mapping Contexts, modifiers and triggers, adding the mapping context, and binding actions by ETriggerEvent. Use when wiring movement/look/jump input, creating IA_/IMC_ assets, binding in C++ or Blueprints, or when the user mentions Enhanced Input, Input Mapping Context, Input Action, IA_/IMC_, or ETriggerEvent.
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Compatibility entry point for React-library work in Octane; routes existing-binding maintenance to update-bindings and actual React implementation ports to octane-react-library-port.
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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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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.
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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.
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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.
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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.
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Use when building or fixing game UI in Unity 6.3: main menu, settings screen (resolution, quality, volume, key rebinding), HUD, health bar, minimap frame; choosing uGUI or UI Toolkit or mixing both; 'UI scales wrong on phones', portrait to 4K, Canvas Scaler, anchors, layout groups collapsing, sort order, UXML/USS, data binding, TextMeshPro or UI Toolkit fonts missing glyphs, localized menus, gamepad navigation, UI draw calls, canvas rebuild spikes, UI tests, or capturing UI to check it.
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Scaffold and deploy Cloudflare Workers with Hono routing, Vite plugin, and Static Assets. Describe project, scaffold structure, configure bindings, deploy. Use whenever the user wants to create a Worker project, set up Hono on Cloudflare, configure D1 / R2 / KV / Queues bindings, or troubleshoot Worker export syntax, API route conflicts, HMR issues, or deployment failures.
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Expert patterns for input handling covering InputMap actions, InputEvent processing, controller support, rebinding, deadzones, and input buffering. Use when setting up player controls, implementing input systems, or adding gamepad/accessibility features. Keywords InputMap, InputEvent, gamepad, controller, rebinding, deadzone, input buffer.
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Expert patterns for input handling covering InputMap actions, InputEvent processing, controller support, rebinding, deadzones, and input buffering. Use when setting up player controls, implementing input systems, or adding gamepad/accessibility features. Keywords InputMap, InputEvent, gamepad, controller, rebinding, deadzone, input buffer.
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Implement ViewBinding, RecyclerView, and XML layouts correctly on Android. Use when changing XML view binding or RecyclerView behavior, including its item animations and layout managers; defer standalone animation or layout-manager questions unrelated to RecyclerView.
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Build and debug Avalonia 11/12 .NET applications with XAML, compiled bindings, MVVM, custom controls, desktop lifetimes, and platform publishing. USE FOR: Avalonia projects, bindings, commands, themes, UI dispatch, trimming, or Native AOT. DO NOT USE FOR: WPF, WinUI, MAUI, Uno, or Avalonia XPF compatibility work. INVOKES: inspect installed versions, implement, and validate on the actual target platforms.
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Guide for implementing Shell-based navigation in .NET MAUI apps. Covers AppShell setup, visual hierarchy (FlyoutItem, TabBar, Tab, ShellContent), URI-based navigation with GoToAsync, route registration, query parameters, back navigation, flyout and tab configuration, navigation events, and navigation guards. Use when: setting up Shell navigation, adding tabs or flyout menus, navigating between pages with GoToAsync, passing parameters between pages, registering routes, customizing back button behavior, or guarding navigation with confirmation dialogs. Do not use for: deep linking from external URLs (see .NET MAUI deep linking documentation), data binding on pages (use maui-data-binding), dependency injection setup (use maui-dependency-injection), or NavigationPage-only apps that don't use Shell.
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Build, review, or migrate Azure Functions in .NET with correct execution model, isolated worker setup, bindings, DI, and Durable Functions patterns. USE FOR: working on Azure Functions in .NET; migrating from the in-process model to the isolated worker model; adding Durable Functions, bindings, or host configuration. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.
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Work on WCF services, clients, bindings, contracts, and migration decisions for SOAP and multi-transport service-oriented systems on .NET Framework or compatible stacks. USE FOR: working on WCF services, bindings, or clients; deciding whether a service should stay WCF or move to modern HTTP APIs; reviewing transport, security, or interoperability. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.
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Build and modernize WPF applications on .NET with correct XAML, data binding, commands, threading, styling, and Windows desktop migration decisions. USE FOR: working on WPF UI, MVVM, binding, commands, or desktop modernization; migrating WPF from .NET Framework to .NET; integrating newer Windows capabilities into a WPF app. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.
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Guidance for implementing CollectionView in .NET MAUI apps — data display, layouts (list & grid), selection, grouping, scrolling, empty views, templates, incremental loading, swipe actions, and pull-to-refresh. USE FOR: "CollectionView", "list view", "grid layout", "data template", "item template", "grouping", "pull to refresh", "incremental loading", "swipe actions", "empty view", "selection mode", "scroll to item", displaying scrollable data, replacing ListView. DO NOT USE FOR: simple static layouts without scrollable data (use Grid or StackLayout), map pin lists (use Microsoft.Maui.Controls.Maps), table-based data entry forms, non-MAUI list controls, CarouselView or BindableLayout questions, platform-specific handler or renderer customization, diagnosing CollectionView bugs in the MAUI framework itself, or general MVVM/binding questions that merely happen to mention a list (use maui-data-binding).
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smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.
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