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Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Generates PSR-6 Cache implementation for PHP 8.5. Creates CacheItemPoolInterface and CacheItemInterface implementations with TTL handling and deferred saves. Includes unit tests.

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This skill should be used when agents generate placeholder tokens like "pseudo-", "mock-", "temporary", "TODO", "demo-", or similar incompleteness markers. Detects substitution patterns in agent OUTPUT and triggers mandatory user interview instead of accepting incomplete work. Activates automatically on any output containing forbidden tokens.

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Library of accessibility personas representing people with various disabilities, impairments, and situational limitations. Use this skill when users ask about disability types, accessibility personas, user needs for specific conditions, how people with disabilities use technology, assistive technology users, or designing for accessibility. Triggers on requests about blindness, deafness, cognitive disabilities, motor impairments, low vision, screen readers, sign language, autism, ADHD, temporary disabilities, or any question about "how would a person with X use this".

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See, Understand, Act on video and audio. See- ingest from local files, URLs, RTSP/live feeds, or live record desktop; return realtime context and playable stream links. Understand- extract frames, build visual/semantic/temporal indexes, and search moments with timestamps and auto-clips. Act- transcode and normalize (codec, fps, resolution, aspect ratio), perform timeline edits (subtitles, text/image overlays, branding, audio overlays, dubbing, translation), generate media assets (image, audio, video), and create real time alerts for events from live streams or desktop capture.

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Generate spectrograms and audio feature visualizations (mel, chroma, MFCC, tempogram, etc.) from audio files via CLI. Useful for audio analysis, music production debugging, and visual documentation.

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Expert in event sourcing, CQRS, and event-driven architecture patterns. Masters event store design, projection building, saga orchestration, and eventual consistency patterns. Use PROACTIVELY for event-sourced systems, audit trail requirements, or complex domain modeling with temporal queries.

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Analyze the threat landscape using MISP (Malware Information Sharing Platform) by querying event statistics, attribute distributions, threat actor galaxy clusters, and tag trends over time. Uses PyMISP to pull event data, compute IOC type breakdowns, identify top threat actors and malware families, and generate threat landscape reports with temporal trends.

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High-performance temporary storage system using Redis. Supports namespaced keys (mema:*), TTL management, and session context caching. Use for: (1) Saving agent state, (2) Caching API results, (3) Sharing data between sub-agents.

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Requires OFOX_API_KEY — create one at https://app.ofox.ai, plus the music file the finished video must carry. Your audio never reaches the API (measured) — the visuals are written to the track's tempo, mood and sections, then your own file is laid on locally at zero cost. One job caps at 30 seconds, so a three-minute song is six jobs minimum and the cost table says that before anything is spent. Use when a user has a specific piece of music and wants visuals for it, e.g. "make a music video for this track", "visuals for my song", "an MV for this instrumental", "generate footage cut to this beat". Do not use for cheap vertical social drafts (shorts-reels), a brand film that happens to have a music bed (seedance-ad-creative), or when there is no particular audio file the finished video has to carry.

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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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