Results for “alignment”

Reduce OpenClaw token usage and API costs through smart model routing, heartbeat optimization, budget tracking, and native 2026.2.15 features (session pruning, bootstrap size limits, cache TTL alignment). Use when token costs are high, API rate limits are being hit, or hosting multiple agents at scale. The 4 executable scripts (context_optimizer, model_router, heartbeat_optimizer, token_tracker) are local-only — no network requests, no subprocess calls, no system modifications. Reference files (PROVIDERS.md, config-patches.json) document optional multi-provider strategies that require external API keys and network access if you choose to use them. See SECURITY.md for full breakdown.

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Consistent radii, pixel-perfect alignment, state coverage, and the details that signal design quality. Use when polishing designs, auditing quality, or evaluating whether a design is ready to ship.

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Implement, review, or improve SwiftUI features using the iOS 26+ Liquid Glass API. Use when asked to adopt Liquid Glass in new SwiftUI UI, refactor an existing feature to Liquid Glass, or review Liquid Glass usage for correctness, performance, and design alignment.

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Improve layout, spacing, and visual rhythm. Fixes monotonous grids, inconsistent spacing, and weak visual hierarchy. Use when the user mentions layout feeling off, spacing issues, visual hierarchy, crowded UI, alignment problems, or wanting better composition.

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Performs a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the user mentions polish, finishing touches, pre-launch review, something looks off, or wants to go from good to great.

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Implement, review, or improve SwiftUI features using the iOS 26+ Liquid Glass API. Use when asked to adopt Liquid Glass in new SwiftUI UI, refactor an existing feature to Liquid Glass, or review Liquid Glass usage for correctness, performance, and design alignment.

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Use this skill when writing, rewriting, or improving marketing copy for any page (homepage, landing page, pricing, feature, product, or about page). This skill produces clear, compelling, and testable copy while enforcing alignment, honesty, and conversion best practices.

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Comprehensive LLM security testing: bias detection, data leakage, prompt injection, jailbreak, alignment testing, adversarial prompts

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Generates complete video ad scripts for 15s, 30s, and 60s formats in Darija (Moroccan Arabic dialect) with shot-by-shot breakdowns, Islamic compliance guidelines, global trend alignment (authenticity, sustainability, UGC), and cultural adaptation for Facebook, Instagram, and TikTok. Includes 4 frameworks including a Moroccan-specific storytelling framework.

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Use when asked to map, crosswalk, align, compare, or gap-analyze any two cybersecurity frameworks, control catalogs, or regulatory requirements using NIST IR 8477 Set-Theory Relationship Mapping (STRM). Triggers on terms like "map controls", "crosswalk", "framework alignment", "gap analysis", or producing a STRM CSV output file.

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End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation efficiency, and stalling. Use when orchestrating a full ribosome profiling pipeline and deciding harvest/dedup/alignment options and which downstream analyses the library can support.

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End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.

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Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.

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Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware Poisson GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via the four-BAM-vector interface (bam_ip + bam_input control; bam_treated_ip + bam_treated_input treatment), ChIPseeker annotation, and the canonical Guitar metagene with stop-codon enrichment as the biological QC anchor. Use when running a complete MeRIP analysis from raw reads, when chaining the constituent epitranscriptomics skills (merip-preprocessing -> m6a-peak-calling -> m6a-differential -> modification-visualization), or when wrapping the pipeline in Snakemake / Nextflow.

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End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Perform a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the work is functionally complete and needs finishing touches—not when the hierarchy, structure, tone, or technical foundation still need major changes.

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Build DPO training pipelines for AI alignment. TRIGGERS - Use when user needs help with ai-dpo-trainer related tasks.

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Windows アプリ開発 (Fluent Design / WinUI 3) のデザインガイドライン。 layout, alignment, spacing, geometry, elevation, breakpoints, Color, materials, Mica, Acrylic, Smoke, Reveal Focus, Reveal Highlight (非推奨), typography, Segoe Fluent Icons, app icons, motion, easing, page transitions, connected animation, parallax, reduce motion, haptics, NavigationView, TitleBar, TabView, CommandBar, menus, keyboard accelerators, access keys, accessibility, high contrast, globalization, RTL, widgets design。

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Rive アニメーションランタイム (Web / React)。 useRive, useRiveFile, useStateMachineInput, RiveComponent, State Machine, Data Binding, ViewModel / ViewModelInstance, Events, Layout / Fit / Alignment, .riv。 @rive-app/canvas / webgl2 / react-canvas / react-webgl2、enableGPUCanvas、 Semantics, Rive CLI。Scripting (Luau), Artboard, Property, Path / Paint / Renderer, WGSL Shaders, GPU pipeline, Node / Layout / Converter スクリプト。

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OpenAI API (developers.openai.com) の運用・管理リファレンス。 Administration API, admin API keys, RBAC, roles, groups, invites, projects, spend limits, audit logs, usage / costs API, Terraform provider (openai/openai), workload identity federation (WIF, OIDC / SPIFFE / X.509 / Idira), moderation API, misalignment monitoring, safety alerts / cases, safety best practices, under-18 guidance, ZDR Private Safety Processing (PSP), production best practices, deployment checklist, cost / latency optimization, fast / ultrafast mode, Realtime API costs。 rate limits・error handling・prompt caching・webhooks は openai-api-core、Codex WIF・管理は openai-codex。

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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