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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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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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An example skill loaded through resources_discover and supplied by the dynamic-resources extension. The material identifies its role as a sample but does not describe a specific task, workflow, or output.

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• Reviewing a sample loaded through resources_discover
• Checking an example supplied by an extension
• Identifying the sample's documented scope

Review repeated event listeners and consolidate them on a shared parent element. This approach, called event delegation, handles dynamically added items and reduces individual listeners while preserving the intended interaction behavior.

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• Fixing interactions on dynamically added list items
• Consolidating listeners across table rows
• Reviewing click target detection

Simulate quantum dynamics, steady states, and spectra with QuTiP 5. The skill guides solver selection and checks physical assumptions, units, state validity, and numerical convergence so local simulation results can be reviewed with their limitations.

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• Simulating quantum dynamics with environmental dissipation
• Choosing a solver for a quantum model
• Checking numerical convergence and state validity

Prepare and run molecular dynamics simulations with OpenMM, then analyze molecular motion with MDAnalysis. Examine protein flexibility, structural changes, and protein–ligand contacts through calculations and plots of simulated trajectories.

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• Investigating protein stability after a mutation
• Measuring structural changes and flexibility
• Tracking protein–ligand contacts

Write and improve C# unit tests with MSTest 3.x/4.x. Covers assertions that check expected results, tests with multiple input sets, asynchronous setup, cleanup, and test organization, with guidance on APIs that differ between versions.

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• Create a C# unit test project
• Test multiple input sets with DataRow or DynamicData
• Update exception checks to modern assertion APIs

Monitor local network traffic for ARP spoofing, where false address mappings can redirect traffic. Use ARPWatch, Wireshark, switch inspection settings, and Python monitoring to flag address changes, duplicate IP claims, gateway impersonation, and unusual ARP volumes.

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• Investigating suspected interception on a local network
• Monitoring changes in IP-to-MAC address mappings
• Checking duplicate IP claims and gateway impersonation

Diagnose GKE TPU virtual machines that remain in repair by checking instance status, host events, and automatic repair history. Understand the impact on grouped TPU nodes and identify recovery steps for the user to apply.

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• Investigating TPU VMs that remain in REPAIRING
• Assessing how a failed node affects a TPU slice
• Checking automatic repair history and failure reasons

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with 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 models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Implement, review, or improve Live Activities and Dynamic Island experiences in iOS apps using ActivityKit. Use when building real-time updating widgets for the Lock Screen and Dynamic Island — delivery tracking, sports scores, ride-sharing status, workout timers, media playback, or any time-sensitive information that updates in real time. Also use when working with ActivityKit, ActivityAttributes, Activity lifecycle (request/update/end), Dynamic Island layouts (compact/minimal/expanded), push-to-update Live Activities, or Lock Screen live widgets.

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The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

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Guide for theming .NET MAUI apps — light/dark mode via AppThemeBinding, ResourceDictionary theme switching, DynamicResource bindings, system theme detection, and user theme preferences. Use when: "dark mode", "light mode", "theming", "AppThemeBinding", "theme switching", "ResourceDictionary theme", "dynamic resources", "system theme detection", "color scheme", "app theme", "DynamicResource". Do not use for: localization or language switching (see .NET MAUI localization documentation), accessibility visual adjustments (see .NET MAUI accessibility documentation), app icons or splash screens (see .NET MAUI app icons documentation), or Bootstrap-style class theming (see Plugin.Maui.BootstrapTheme NuGet package).

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Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

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Think and work like an expert Geodynamics & Tectonics Scientist. Use when a task calls for Geodynamics & Tectonics Scientist judgment. Reasons from plate kinematics, lithospheric rheology, and interseismic-versus-coseismic strain partitioning through GAMIT/GLOBK and MintPy geodesy, Okada/viscoelastic slip inversion, OxCal paleoseismic chronologies, ASPECT mantle modeling, and OpenQuake/USGS NSHM hazard while treating InSAR atmospheric delay, monument instability, unmodeled postseismic afterslip, and incompatible-timescale rate stacking as first-class failure modes.

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Think and work like an expert Fluid Dynamicist. Use when a task calls for Fluid Dynamicist judgment. Reasons from Navier–Stokes and dimensionless scaling through RANS/LES/DNS selection, mesh/y+ strategy, OpenFOAM/Fluent workflows, and MMS + ASME V&V 20 / PIV validation.

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Think and work like an expert Aerodynamicist. Use when a task calls for Aerodynamicist judgment. Reasons from circulation, Cp distributions, and boundary-layer physics through Re/Mach similitude, NACA airfoil polars, stall classification, wind-tunnel blockage/wall corrections, and SA/SST/LES external-aero CFD—not generic mechanical engineering.

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Think and work like an expert Astrodynamicist. Use when a task calls for Astrodynamicist judgment. Reasons from two-body plus perturbation force models through Cowell/Encke propagation, batch LS and EKF orbit determination, SPICE/Horizons ephemerides, CCSDS OEM/CDM exchanges, and TEME–GCRF frame discipline while treating drag, stale TLE/B*, and covariance frame mismatch as first-class failure modes.

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Perform dynamic security testing against running web applications and APIs to discover vulnerabilities through active probing and fuzzing. Use when the user requests dynamic application security testing or provides relevant inputs for this workflow.

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Classical control and system dynamics for engineered systems — feedback and closed-loop control, transfer functions and block diagrams, poles/zeros and stability, time-domain response (rise time, overshoot, settling time), PID controllers and tuning, and frequency response (Bode plots, gain and phase margin). Traces feedback control from the flyball governor to modern controllers. Use when analyzing feedback loops, designing or tuning a PID controller, assessing stability from poles or margins, or characterizing transient response of a dynamic system.

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Analyzes securities lending market with borrow cost, short interest dynamics, and fail-to-deliver monitoring. Use when analyzing lending markets, tracking borrow costs, or evaluating short selling dynamics.

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Evaluates implied volatility surfaces with skew analysis, term structure dynamics, and surface fitting methodologies. Use when analyzing vol surfaces, assessing skew dynamics, or calibrating volatility models.

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Analyze the dynamics of diffusion processes using stochastic differential equations, Fokker-Planck equations, first-passage time distributions, and parameter sensitivity analysis. Use when deriving probability density evolution for a continuous-time diffusion process, computing mean first-passage times for bounded diffusion, analyzing how drift and diffusion parameters affect process behavior, or validating closed-form solutions against stochastic simulation.

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