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Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.

日本語の概要は準備中です。原文の説明を表示しています。

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

日本語の概要は準備中です。原文の説明を表示しています。

Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

日本語の概要は準備中です。原文の説明を表示しています。

Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

日本語の概要は準備中です。原文の説明を表示しています。

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

日本語の概要は準備中です。原文の説明を表示しています。

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

日本語の概要は準備中です。原文の説明を表示しています。

Use when a carrier asks whether to buy or lease their next tractor (or trailer), comparing full-service lease (Ryder, Penske, NationaLease), capital lease, finance lease, walk-away open-end lease, or cash purchase. Covers tax treatment, residual risk, maintenance bundling, balance-sheet impact, and cash-flow modeling.

日本語の概要は準備中です。原文の説明を表示しています。

Defensive counterpart to federated-harbor-redteam: closes the smells that red team opens against The Federated Harbor whitepaper. Federation-specific defenses for cross-harbor primitives — mechanization commitments, scope hedges, cross-paper dependency formalization, pre-emptive analogies (CT, Macaroons, atomic swaps), and defense-in-depth framing (refuses vs prices). Use during a versioned red-vs-white round; pairs with federated-harbor-redteam. NOT for ad-hoc code review, NOT for the Anchor or Bonded papers (use whitehat-defense).

日本語の概要は準備中です。原文の説明を表示しています。

Expert API designer for REST, GraphQL, gRPC architectures. Activate on: API design, REST API, GraphQL schema, gRPC service, OpenAPI, Swagger, API versioning, endpoint design, rate limiting, OAuth flow. NOT for: database schema (use data-pipeline-engineer), frontend consumption (use web-design-expert), deployment (use devops-automator).

日本語の概要は準備中です。原文の説明を表示しています。

Author a pull request an AI coding agent can actually get merged: a scoped, coherent diff; a Summary and Test Plan backed by real evidence; correct triage of required-and-blocking CI gates versus external/advisory checks (e.g. a Cloudflare Pages preview build); draft-while-WIP discipline; named fixup commits for real review findings; and a clean landing through a merge queue without force-pushing or bypassing branch protection. Use when opening, updating, triaging red CI on, or landing an agent-authored GitHub PR. NOT for this repo's internal release ceremony, actor embodiments, or contributor mirror-sync mechanics (use port-daddy-internal-dev), tracking backlog/issue lifecycle across a board (use agent-issue-tracker-workflow), or deciding what to build next / sequencing a roadmap (use legible-roadmap-with-sidequests).

日本語の概要は準備中です。原文の説明を表示しています。

Data structures and serialization formats for agent-to-agent communication. Covers message envelopes, structured output schemas, capability declarations, task handoff payloads, error/retry signaling, and context windows as data structures. Compares the version-pinned A2A, MCP, and JSON-RPC role boundaries covered by this bundle; OpenAI and LangChain-specific APIs require their own current sources. Teaches when to use rigid schemas versus free-form content with validation, typed versus untyped boundaries, and streaming versus batch. Activate on: "agent message format", "agent communication schema", "agent-to-agent protocol", "A2A protocol", "MCP message format", "structured output for agents", "agent interop", "interchange format", "agent serialization", "task handoff format", "capability declaration". NOT for: what agents say to each other (use agent-conversation-protocols), orchestration topology (use multi-agent-coordination), building agent infrastructure (use agentic-infrastructure-2026).

日本語の概要は準備中です。原文の説明を表示しています。

Configure an AI agent to send OpenTelemetry traces to Coval. Use when a user wants to add Coval tracing, instrument an agent for simulations or conversation monitoring, make traces show up in Coval, handle SIP/PSTN/WebSocket trace correlation, or replace the one-command wizard with a security-reviewable manual setup.

日本語の概要は準備中です。原文の説明を表示しています。

Troubleshoot Coval OpenTelemetry trace ingestion, missing trace UI, sparse traces, bad simulation or conversation correlation, auth/org errors, oversized payloads, duplicate spans, and production debugging with Trace Search.

日本語の概要は準備中です。原文の説明を表示しています。

Recommend, create, preview, and attach Coval trace-based metrics from OpenTelemetry spans. Use when a user has Coval traces and wants custom trace metrics, trace-aware LLM judge metrics with include_traces, latency, token usage, provider failures, tool behavior, vertical-specific workflow signals, or production monitoring based on trace attributes.

日本語の概要は準備中です。原文の説明を表示しています。

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

日本語の概要は準備中です。原文の説明を表示しています。

Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation.

日本語の概要は準備中です。原文の説明を表示しています。

Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change.

日本語の概要は準備中です。原文の説明を表示しています。

The WindowPanel component and Window Manager. Use when a window won't drag/resize/minimize, the tray is missing, window state doesn't persist, rendering `<WindowPanel>` on a page, or editing features/window-panels/** or windowManagerSlice.ts. NOT for opening/registering overlays (use overlay-system).

日本語の概要は準備中です。原文の説明を表示しています。

The standing order for local git state in every AI Matrx repo — zero worktrees, zero local branches, zero dirty files, zero open PRs, everything merged to origin/main, and no code ever lost. Use when you find a worktree, a local branch, a stale checkout, an unpushed commit, or a dirty tree in any repo under /Users/armanisadeghi/code, when asked to "clean up", "unify", "merge everything", or when you are tempted to create a worktree or branch. Works without any access to Arman.

日本語の概要は準備中です。原文の説明を表示しています。

Next.js route metadata, per-route favicons, OpenGraph, and Twitter cards. Use when adding a route or layout, adding a favicon or social share image, auditing missing metadata, naming tab titles, or touching createRouteMetadata, createDynamicRouteMetadata, generateFaviconMetadata, or titlePrefix.

日本語の概要は準備中です。原文の説明を表示しています。

No-trace removal recipe for a window panel or overlay. Use when deleting, killing, or retiring a window/overlay, or consolidating X into Y and deleting X ('kill this panel', 'remove the X window'). NOT for adding or opening an overlay (use overlay-system).

日本語の概要は準備中です。原文の説明を表示しています。

Cross-app save-to-notes components and patterns. Use when adding save-to-notes to a feature, wiring overlay note capture, editing features/notes/actions/ or its consumers, or using QuickCaptureButton, SaveToScratchButton, SaveSelectionButton, QuickNotesSheet, CategoryNotesModal, or openSaveToNotes.

日本語の概要は準備中です。原文の説明を表示しています。

Recipe for THE DOOR LAW (every record the UI names opens; every detected problem ships its fix) and THE INVENTORY LAW. Use before building or fixing a surface that names a record or flags a problem (cell, row, dialog, badge, warning, id, count), or on 'no link to X', 'why can't I click this', 'dead end', EntityRef, peek. NOT for page chrome (use core-route-headers).

日本語の概要は準備中です。原文の説明を表示しています。

The matrx-frontend side of the matrx-extend Chrome extension bridge. Use when adding or changing a FRONTEND_RPC action handler, a window-panels deep-link the extension opens, a headless API route it calls, or debugging a silent chrome.runtime.sendMessage or Broadcast round-trip. NOT for code in matrx-extend, matrx-local, or aidream (each has its own connect-* skill).

日本語の概要は準備中です。原文の説明を表示しています。