Results for “logs”

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.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Run build, deploy, inspect, and fix loops for .NET MAUI apps that already have MAUI DevFlow integrated. USE FOR: launching MAUI apps, selecting devices or emulators, waiting for or recovering agent connections, broker/port/adb connectivity issues, visual tree inspection, screenshots, UI interaction, Blazor WebView CDP debugging, reading DevFlow logs, and iterative app debugging. DO NOT USE FOR: first-time DevFlow package setup (use maui-devflow-onboard), or generic desktop automation unrelated to MAUI. INVOKES: maui devflow CLI, dotnet CLI, Android adb/android tools, and Apple simctl tools.

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Use this skill when the user asks about logging / log hauling operations — short-haul exemption specifics for logging, log truck securement, axle weights, state-by-state logging permits (especially OR, WA, ID, BC), bunk + stake configurations, and how logging fits into FMCSA + state rules. Reference 49 CFR 393 for cargo securement of logs.

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Implementing distributed tracing with W3C Trace Context — the byte-precise `traceparent` and `tracestate` header formats, OpenTelemetry's W3CTraceContextPropagator as the modern default (replacing X-B3-* and X-Datadog-*), head vs tail sampling, and HTTP→SQL trace propagation via sqlcommenter. Grounded in the W3C REC and OpenTelemetry specs. NOT for OTel metrics/logs pipelines, vendor backend setup (Datadog/Honeycomb/Jaeger/Tempo), or browser RUM tracing.

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Runtime enforcement of file system boundaries and tool access restrictions. Blocks unauthorized operations and logs violations. Activate on 'enforce scope', 'access control', 'boundary enforcement', 'tool restrictions', 'runtime security'. NOT for validation (use dag-permission-validator) or isolation management (use dag-isolation-manager).

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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Interprets GitHub Actions run status and logs, diagnoses CI failure patterns, and suggests targeted fixes. Handles dependency install failures, test timeouts, build OOM, flaky tests, and workflow misconfigurations. Activate on: 'CI failing', 'build broken', 'workflow error', 'GitHub Actions debug', 'flaky CI', 'pipeline timeout', 'CI red'. NOT for: writing new workflows from scratch (use github-actions-pipeline-builder), CI caching strategy (use ci-cache-optimizer), deployment orchestration (use devops-automator).

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Design a normalized, machine-readable "work receipt" that answers what changed, why, by whom, and with what validation, for any AI-coding-agent task regardless of backend (Claude Code, Codex, Cursor, Aider, CI, or homegrown). Use when defining a receipt schema, normalizing heterogeneous agent logs into one evidence shape, gating PR merges on artifact-backed proof, or designing an OSS maintainer's fast-reject/fast-merge workflow. NOT for validating a DAG node's output against its own schema (use output-contract-enforcer), continuous runtime monitoring of a live coordination daemon (use runtime-verification-for-agents), or general Port Daddy claims/notes/salvage mechanics (use port-daddy-agent-skill).

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Cryptographic security for agentic systems — zero-trust agent networking, signed message envelopes (JWS/JWE), capability-based security (ocaps), Merkle tree audit trails, WASM sandboxing, and formal verification. Covers CLI dev tool security, mTLS between agents, permission boundaries (least privilege for AI agents), and supply chain security for skills/plugins. Activate on: "agent security", "zero trust agents", "secure agent communication", "capability-based security", "ocap", "signed messages between agents", "agent audit trail", "sandbox agent execution", "agent permissions", "mTLS agents", "cryptographic verification", "agent supply chain", "OWASP agentic", "prove agent did X", "tamper-proof agent logs". NOT for: application-level SAST scanning (use security-auditor), network firewall rules (use infrastructure), SOC2/HIPAA compliance (organizational), or prompt injection defense (use prompt-engineer).

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Overlay system on @ai-matrx/summon: dialogs, sheets and windows declared once in features/overlays/definitions, opened by dispatch. Use when opening, adding, debugging an overlay, or touching features/overlays/**, SummonHost, defineOverlay, useOpenX. NOT for WindowPanel chrome (use window-panels).

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A live demo or admin page shipped with every feature whose results the user would otherwise not see. Use when building or extending a server-side capability, service, registry, or pipeline, or adding a backend endpoint or feature with no UI, whose output only shows in logs, the DB, or an agent run, or when the user says there's no way to see it or asks 'how do I test this'.

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Finds what changed in Claude — docs, release notes, changelogs, GitHub and community posts on Claude Code, claude.ai, Cowork, the API and models — and turns each change into adopt rows for your setup, plus a fit card for a new model or feature and a monthly bench of your skills against public skill and plugin repos (build, adopt or skip). Trigger on what changed since a date or version, a weekly sweep, features worth adopting, a feature that broke unannounced, a stale model table, what a new model or feature is good for, or how your skills compare with popular or little-known skill and plugin repos; or say scoutwright (sweep, since, watch, adopt, fit, bench, sources, refresh). Outside research is researchscribe's; applying a row, skillwright's; config, rigwright's; schedules, agentwright's; tier picks, promptwright's.

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Query a running Convex app's logs + health in natural language (official MCP): failures, slow/expensive functions, deploy causality — scoped, evidence-backed, with a dashboard deep link.

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[22] UNDERSTAND. Deep research from all sources — internal (code, git, logs) AND external (web, docs, best practices). Use when choosing libraries, investigating solutions, understanding legal/technical questions, comparing approaches, or anytime you need comprehensive knowledge from both project context and world knowledge. Triggers on "research", "investigate", "find best approach", "what do others do", "compare options", or complex questions requiring multiple sources.

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AI-assisted video editing workflows for cutting, structuring, and augmenting real footage. Covers the full pipeline from raw capture through FFmpeg, Remotion, ElevenLabs, fal.ai, and final polish in Descript or CapCut. Use when the user wants to edit video, cut footage, create vlogs, or build video content.

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Azure Monitor OpenTelemetry Exporter for Java. Export OpenTelemetry traces, metrics, and logs to Azure Monitor/Application Insights.

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Azure Monitor Ingestion SDK for Java. Send custom logs to Azure Monitor via Data Collection Rules (DCR) and Data Collection Endpoints (DCE).

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Auto-instrument Node.js applications with distributed tracing, metrics, and logs.

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AI-assisted label triage for NVIDIA/NemoClaw issues and PRs. Reads triage-instructions.md at runtime for consistent label guidance. Supports single-item mode (give it a number) and batch mode (fetches up to 50 unlabeled open items). On approval, applies labels and an optional triage comment via gh CLI, then logs the session to the daily-rhythm activity folder. Trigger keywords - triage, label issues, suggest labels, batch triage, triage issue, triage PR, label this, what labels.

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Inspects sandbox health, traces agent behavior, and diagnoses problems. Use when monitoring a running sandbox, debugging agent issues, or checking sandbox logs. Trigger keywords - monitor nemoclaw sandbox, debug nemoclaw agent issues.

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