「proven」の検索結果

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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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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Real tests around a big code change: written first, proven to fail on a planted break, run by a fresh agent in the live product before and after. Use when told to use safety-net, or before a change wide enough that one agent cannot see every way it breaks. NOT for one test (forcing-function-tests).

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Rules for SKILL.md files that trigger, fit, and are proven. Use when creating a SKILL.md, rewriting its description, splitting an oversized SKILL.md, or editing one because an agent ignored, misread, or never fired it.

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Rehearse a live-app schema change + backfill on a snapshot-seeded preview deployment, verify, then promote the proven change to prod with the snapshot as rollback.

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Systematically finds and fixes bugs using proven debugging techniques. Traces from symptoms to root cause, implements fixes, and prevents regression.

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Master proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design to build maintainable, testable, and scalable systems.

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Validate ideas, build strategy, and make decisions with proven frameworks.

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Verify supply chain integrity for AI agent plugins, tools, and dependencies. Use this skill when: - Generating SHA-256 integrity manifests for agent plugins or tool packages - Verifying that installed plugins match their published manifests - Detecting tampered, modified, or untracked files in agent tool directories - Auditing dependency pinning and version policies for agent components - Building provenance chains for agent plugin promotion (dev → staging → production) - Any request like "verify plugin integrity", "generate manifest", "check supply chain", or "sign this plugin"

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5 proven agent skill design patterns (Tool Wrapper, Generator, Reviewer, Inversion, Pipeline) from Google's ADK. Build reliable, composable skills with templates, decision trees, and composition guides. Stop cramming logic into prompts—use structured patterns instead.

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12306-specific knowledge for booking train tickets via the Android app. Covers UC WebView virtual list behavior, proven booking flow, and common pitfalls. Uses appium-android-adb bridge OR direct uiautomator2 for all interaction.

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Run a non-destructive open-source, npm, or public release readiness checklist covering package metadata, provenance, license, internal artifact exposure, and dry-run evidence; complements security, shipping, and sanitizer reviews, and must not publish, delete, rewrite history, or mutate release state.

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Analyze source data, tables, CSV/XLSX extracts, metrics, or experiment results with explicit data-authenticity checks. Use for profiling, cleaning assumptions, statistical summaries, segmentation, trend analysis, or "analyze this data"; do not use for spreadsheet file surgery, chart design only, database migrations, or claims without data provenance.

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Produces build artifacts with Software Bill of Materials (SBOM) and supply chain metadata for security and compliance. Use for "artifact publishing", "SBOM generation", "supply chain security", or "build provenance".

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Hunt CORS Misconfiguration — origin-reflection with credentials, null-origin trust, subdomain-regex bypass (unanchored vs unescaped-dot vs prefix-only), pre-flight (OPTIONS) gating bypass, postMessage origin checks. High only when an attacker-controlled origin can perform a CREDENTIALED cross-origin read of sensitive data and you have proven it in a browser. Use when testing API endpoints, SPAs, or any app emitting Access-Control-* headers.

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Analyzes and optimizes pricing strategy using proven frameworks

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Write compelling business proposals that win deals. Structured templates for service proposals, project bids, and partnership pitches with proven conversion frameworks.

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Generate conversion-focused landing page copy section by section using proven frameworks

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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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Secure the path from an inbound event (webhook, email, SMS, GitHub comment, file, cron) to an agent spawn in the Port Daddy fleet. Use when wiring trigger sources to agents, reviewing the io-wiring registry, adding a trust/permission gate, hardening output sinks (SSRF/path traversal), scoping tools by provenance, or proving the spawn path is safe against prompt-injection → tool-abuse. Encodes ADR-0093 and the red-team threat model. NOT for generic Coast Guard sandboxing (ADR-0050), the macaroon push-grant gate alone (ADR-0053), or non-fleet code.

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Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.

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Designs, reconciles, and reviews an end-to-end Drydock program for safely staging agent runtimes: immutable worktree provenance, disposable VM containment, typed effect brokerage, global body accounting, resurrection, subscription-capacity economics, context compaction, operator control, evidence, and promotion. Use when several Drydock contracts must compose into one architecture, implementation hypertree, diagram set, or release plan. NOT for launching Port Daddy, running an untrusted subject, replacing focused containment/resurrection/capacity audits, or treating a design packet as runtime authority.

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Classify every destructive/gated action an agent body can attempt (git, filesystem, network, shell, github) into block/approve/allow tiers, and audit whether the pre-tool and post-tool governance backing that classification is real: blocked actions proven zero-side-effect by a negative fixture, every denial backed by a receipt and a transcript event, every block-tier denial paired with a safe alternative, and no unmanaged or same-UID body ever marked "contained." Use when building or reviewing Agent Harbor's C5 governance gate (destructive git blocker, approval request/result, denial receipts), gating a new tool surface before it can run destructive commands, or auditing whether an existing "destructive-action blocked" claim actually has evidence behind it. NOT for proving an existing sandbox boundary actually contains an adversary once an action is isolated (use sandboxed-adversarial-test-harness), deciding where in a DAG to place a human review node or designing the approval UX itself (use human-gate-designer), or designing the general work-receipt schema across an entire agent task (use agent-work-receipt-designer).

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