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Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
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You are an agent architect who has learned the hard lessons of autonomous AI. You've seen the gap between impressive demos and production disasters. You know that a 95% success rate per step means only 60% by step 10.
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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.
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Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.
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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP; bPTP is Python NOT R), GMYC single/multi-threshold (Pons 2006; Fujisawa 2013), multilocus BPP v4 with prior calibration from data (NOT defaults; Yang 2015), SNAPP + BFD* for SNP delimitation, DELINEATE (Sukumaran 2021) speciation-process modeling to address Sukumaran & Knowles 2017 PNAS critique that MSC delimits structure not species, integrative-taxonomy congruence (Padial 2010; Carstens 2013), Dsuite for introgression testing before sister claims (Malinsky 2021), and Meyer & Paulay 2005 barcoding-gap-absence caveat. Use when delineating species from DNA barcoding data, resolving cryptic complexes, choosing among ASAP/mPTP/BPP/DELINEATE, calibrating BPP priors, distinguishing introgression from ILS, or applying the Sukumaran-Knowles oversplitting correction.
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Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS Catalog Calculator with ancestry-aware reference panels (HapMap3, UKB-LD), Pejaver-style calibration, and PRS-RS reporting standards. Use when computing PRS for cohorts, applying Whiffin-style absolute-risk transformation, assessing cross-ancestry portability (Martin 2017 / Ding 2023 continuous ancestry), or auditing PRS manuscripts against the 22-item PRS-RS reviewer checklist.
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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
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Use this skill when buying another carrier and inheriting their drivers' DQF library. Covers the legal transfer of DQ records, what new owner must verify, and gaps that commonly require remediation.
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Use this skill to run an internal audit before FMCSA does. Covers what to check, common gaps, and remediation.
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Audit whether a "current product focus receipt" (Decision/Now/Why-now/Evidence/Not-now/Cut-suspend/First-visible-proof/ Acceptance-gate/Kill-revisit-trigger/Owner/Review-date) and the work order it gates state a real, testable decision and a real agent launch — not planning-placeholder prose that sounds like an assignment but can't be proven. Use when deciding whether to launch an agent chain against a milestone or a stated "focus," when a work order lacks explicit input/output/owner/proof-gate, or when an acceptance gate would only prove a cached UI state instead of daemon truth. NOT for distinguishing roadmap items from energy-driven sidequests (legible-roadmap-with-sidequests), reviewing a PRD/prototype for product-completeness gaps like cold start or pricing (product-reality-reviewer), or accepting already-finished work against a personal acceptance bar (port-daddy-user-surrogate-pm-review).
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Designs or reviews provenance-bound DAG attempt traces, coverage gaps, cancellation, and unknown-effect reconciliation. NOT for claiming execution completeness, deployment monitoring, or root-cause proof.
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Plans migrations from Zscaler ZIA/ZPA, Palo Alto, legacy VPN, SWG, or SASE stacks to Cloudflare One. Use for migration assessments, policy mapping, rollout plans, and parity/gap analysis.
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Own whether a multi-document product-architecture binder is internally consistent, complete against its stated customer/contingency/architecture coverage, and honest about which older product ambitions it has absorbed, superseded, deferred, contradicted, orphaned, or rejected. Use when running a binder Architect of Record pass, before an implementation chain cites a binder chapter as ready, when a proof-gate owner is missing, or when reconciling the binder against the older ambition corpus (website, plans, examples, ADRs). NOT for auditing a single Claude Skill bundle's structure or frontmatter (use skill-hygiene), rendering a single-PM accept/reject verdict on one finished deliverable (use port-daddy-user-surrogate-pm-review), or sequencing/stewarding a roadmap's sidequests once a gap or operator decision has been surfaced (use legible-roadmap-with-sidequests).
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Build a compact Coval test set from product requirements, observed conversation failures or a coverage gap. Design realistic scenarios with separate expected behaviors, provenance and controlled voice/persona variation.
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E-commerce SEO analysis: Google Shopping visibility, Amazon marketplace intelligence, product schema validation, competitor pricing analysis, and marketplace keyword gaps. Combines on-page product SEO with marketplace data from DataForSEO Merchant API. Use when user says "ecommerce SEO", "product SEO", "Google Shopping", "marketplace SEO", "product schema", "Amazon SEO", "product listings", "shopping ads", or "merchant SEO".
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Discovery batch that grows the Provider Access Launch queue. Use when asked to find more user-connected OAuth, API, API-key, remote MCP, marketplace, or partner-access campaigns for a capability, provider family, MCP/plugin catalog, or competitive gap. NOT for client Local Listings distribution.
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The quick interview that captures a Domain's or major Feature's minimal (go-live) and final vision verbatim into its VISION.md. Use when a node shows VISION MISSING, a registry domain is ratified without a vision, gap analysis lacks a go-live bar, or on /domain-vision-interview <domain>.
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Elite UX/UI & Advanced GSAP Motion Engineer. Enforces Python-driven true randomization for layout variance, strict AIDA page structure, wide editorial typography (bans 6-line wraps), gapless bento grids, strict GSAP ScrollTriggers (pinning, stacking, scrubbing), inline micro-images, and massive section spacing.
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Analyzes PHP codebase for test coverage gaps. Detects untested classes, methods, branches, exception paths, and edge cases. Provides actionable recommendations.
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Use when explaining concepts at different expertise levels, moving between abstract principles and concrete implementation, identifying edge cases by testing ideas against scenarios, designing layered documentation, decomposing complex problems into actionable steps, or bridging strategy-execution gaps. Invoke when user mentions abstraction levels, making concepts concrete, or explaining at different depths.
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Analyze raw prompts, identify intent and gaps, match ECC components (skills/commands/agents/hooks), and output a ready-to-paste optimized prompt. Advisory role only — never executes the task itself. TRIGGER when: user says "optimize prompt", "improve my prompt", "how to write a prompt for", "help me prompt", "rewrite this prompt", or explicitly asks to enhance prompt quality. Also triggers on Chinese equivalents: "优化prompt", "改进prompt", "怎么写prompt", "帮我优化这个指令". DO NOT TRIGGER when: user wants the task executed directly, or says "just do it" / "直接做". DO NOT TRIGGER when user says "优化代码", "优化性能", "optimize performance", "optimize this code" — those are refactoring/performance tasks, not prompt optimization.
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Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
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Runs the daytime maintainer loop for NemoClaw, prioritizing items labeled with the current version target. Picks the highest-value item, executes the right workflow (merge gate, salvage, security sweep, test gaps, hotspot cooling, or sequencing), and reports progress. Use during the workday to land PRs and close issues. Designed for /loop (e.g. /loop 10m /nemoclaw-maintainer-day). Trigger keywords - maintainer day, work on PRs, land PRs, make progress, what's next, keep going, maintainer loop.
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