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Turn one line ("a turbofan jet engine", "a mechanical watch", "an LVAD heart pump") into a photoreal, physics based, interactive 3D simulation of that machine in a single HTML file, plus a 20 to 30 second film to post it. Real proportions in metres, real materials (PBR metals, paints, polymers, glass), studio lighting with soft shadows, moving parts driven by a small solver that computes real numbers (thrust, torque, rpm, flow, pressure, efficiency), and modes to explode it, cut it open with clean section caps, x-ray it, slow it down, label it and break it. Use this whenever someone asks to build, simulate, visualise, explain or "show how X works" for any machine, engine, mechanism, device, instrument or piece of hardware, wants an interactive 3D model or a cutaway, or wants a video of a machine for a post, even if they never say "simulation" or "three.js".

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Summarize the architecture of code generated by a single retort run. Produces module-level structure, interfaces, and control flow in a form suitable for cross-run comparison — not a full codebase-summary.

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Evaluate a single retort experiment run. Score the generated code against the task's TASK.md requirements, run its build and tests, compute metrics, and emit a structured evaluation report plus a machine-readable findings file.

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Med-sector overview across med.medicines_biotech and med.medical_devices with med trends, catalysts, FDA-decision context, and a cross-sector ripple map (quantified sign/magnitude per name). Use to frame any biotech/pharma/device analysis before diving into a single name.

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Institutional-grade equity research skills for AI agents. 80 Claude-type skills across 14 verticals (equity-research-core, models-and-pitches, bio-pharm, scenarios, quantitative-analysis, idea-generation, options-derivatives, business-intelligence, industry-analysis, macro-strategy, portfolio-strategy, technical-analysis, risk-and-psychology, trading-as-business) powered by agentii.ai's agent-use-ready SEC filing data plane — SEC filings and 15K+ earnings call transcripts, 15.99M XBRL facts, and company profiles for 1,146+ US-public-equity tickers. Features the three-layer retrieval protocol (Document Discovery → Page Map → Deep Read, with deep-outline escalation) — measured, not asserted: 97.5% saved against a sequential read, and the page map itself is 10.0% of one (spec 062 T030, 2026-09-23) — server-side parallel multi-period search via search_cross_period, a full Excel/PPT generation pipeline with 3-tier office backend support, and the spec-046 governance layer (constitution, thesis and single-skill modes, mechanical gates, and a template-owned disclaimer on generated reports).

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Guide structured design thinking through 5 progressive levels before any code is written. Levels: Capabilities, Components, Interactions, Contracts, Implementation. Use when building new features, refactoring significant code, designing modules, or when the user says 'design this', 'architect this', 'let's think before coding', 'walk me through the design', or 'whiteboard this'. For simple utilities enter at Level 4 (Contracts), for single-component tasks at Level 2 — see Complexity Calibration. Do not use for quick bug patches.

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Generate persistent, explorable 3D worlds/environments with Marble by World Labs — from text, a single image, multiple images, video, or a 360 panorama, plus coarse-structure blocking with Chisel. Use this skill when a task needs a navigable 3D scene, VR/immersive backdrop, virtual-production environment, previz set, game-blockout, or web/engine-ready Gaussian splat or mesh, and you must choose an input mode, a Marble model, an export format, and a plan/API route, then review world quality. Covers the Marble web app and the World API, editing/expansion, output formats and what each supports downstream, import into Unity/Unreal/Blender/Houdini/web, pricing/credits, capability limits, and rights/licensing. Not for flat text-to-image, text-to-video clips, or real-time on-the-fly world models (Marble outputs are downloadable, static 3D environments).

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Plan, prompt, execute, troubleshoot, and quality-control Black Forest Labs FLUX image generation and editing across the BFL direct API and licensed local/open-weight deployments. Use for FLUX.2 model selection, text-to-image, single- or multi-reference editing, typography, exact-color work, mask-based erase/inpainting, outpainting, API integration, reproducibility, deployment licensing, and production rights or safety decisions; also use when migrating or maintaining legacy FLUX.1/FLUX1.1 workflows.

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Use this skill when planning, capturing, processing, validating, troubleshooting, or exporting markerless human motion capture with Move AI products, including Move One single-camera workflows and Genesis multi-camera studio systems. It covers provider selection, setup, calibration, wardrobe and lighting constraints, documented multi-person operation, processing, cleanup, skeleton and retargeting choices, DCC/game-engine export, data management, consent, and privacy. Do not use it for general keyframe animation, non-Move mocap systems, 3D asset generation, or generic animation cleanup unrelated to Move AI outputs.

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Provider-independent production workflow for AI agents creating music videos, lyric videos, visualizers, performance/narrative/dance videos, social cutdowns, album or single launch assets, and generated-media clips synchronized to songs. Use when planning, directing, prompting, editing, reviewing, or delivering video content built around a recorded song, artist performance, lyrics, beat timing, choreography, platform variants, music rights, likeness consent, accessibility, or synthetic-media disclosure.

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Produce audio-first podcast episodes with generative tools — design the show and episode format (interview, narrative, news brief, two-host conversational), write scripts for the ear, decide between fully-synthetic and hybrid (recorded human + synthetic) production and meet the disclosure duty each triggers, cast and direct multi-voice TTS for consistency and chemistry, build episode structure (cold open, intro/outro, segments, ad slots), assemble and edit, clear music and SFX rights, hit podcast loudness and delivery standards, ship metadata/chapters/transcripts through RSS, and pass platform AI-content policy and QA before publishing. Use this skill whenever the deliverable is a podcast episode or a podcast show bible, or when an agent must make production, rights, disclosure, or delivery decisions for spoken-word audio. Not for music tracks, single-voice notification prompts, or video where picture leads (route audio-for-video to a video skill).

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All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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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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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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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.

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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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Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk or single-cell expression data. Use when finding co-expression modules, identifying hub genes, or relating gene networks to clinical or experimental variables.

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End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

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Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when inferring ligand-receptor interactions between cell types.

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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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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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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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