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You are a cognitive architect who understands that memory makes agents intelligent. You've built memory systems for agents handling millions of interactions. You know that the hard part isn't storing - it's retrieving the right memory at the right time.
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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.
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Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.
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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.
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Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of current Kaleido static-export model (post-orca-EOL), HTML file-size bloat, and the limits of interactive-only output for journal submission. Use when producing zoomable/hoverable plots for notebook EDA, supplementary HTML, dashboards, or animated time-course / iteration visualizations.
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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.
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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.
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Add MAUI DevFlow to a .NET MAUI project with agent package references, MauiProgram.cs registration, Blazor WebView support, GTK variants, Central Package Management guidance, and verification commands. USE FOR: first-time DevFlow setup, reviewing what files to edit, choosing DevFlow packages, or continuing after `maui devflow init` installs skills. DO NOT USE FOR: troubleshooting an already-integrated app that cannot connect, iterative app debugging, UI inspection, or generic MAUI build failures (use maui-devflow-debug). INVOKES: maui devflow CLI and dotnet CLI.
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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 how to design or improve a Preventive Maintenance (PM) program for a fleet — mileage vs time intervals, A/B/C/D inspection levels, ATA standards, common PM tasks, scheduling software, cost tracking, and how PM affects roadside inspections + CSA scores. Reference ATA Equipment Maintenance Council standards.
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Use this skill when the user asks about CMV roadside inspection levels (Level I through Level VIII), what each level inspects, average inspection times, CVSA decal eligibility, what triggers a level upgrade, and how to coach drivers through a roadside inspection. Reference CVSA North American Standard Inspection Program.
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Use when a driver has been involved in a crash — regardless of preventability or injury — and the carrier needs to handle the immediate, post-investigation, and return-to-work phases. Covers trauma response, post-accident testing under 49 CFR 382.303, paid time off, retraining, light duty, and re-entry planning.
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Use this skill for training drivers on effective pre-trip inspection technique. Covers the comprehensive walk-around, time investment, and common areas drivers miss.
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Use when a driver has been disqualified or is at risk of disqualification — major offense convictions (DUI, leaving the scene, drug trafficking with CMV), serious traffic violations, RR-grade-crossing violations, imminent-hazard out-of-service, or Clearinghouse positive-test prohibited status. Also use when planning a return-to-duty pathway, SAP process, or reinstatement timeline. Covers 49 CFR 383.51, Part 40 Subpart O, and Part 391.15.
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Use this skill when a driver needs to edit their own ELD record. Covers what edits are allowed, what edits trigger annotations, the unassigned-driving-time procedure, and when carriers must accept or reject driver edits.
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Use this skill when a driver does not meet federal medical standards and needs to apply for a variance. Covers application steps, required documentation, and review timeline.
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Use this skill when a driver encounters adverse weather, road, or traffic conditions and needs to extend driving time. Covers eligibility criteria, the 2-hour maximum extension, documentation requirements, and what does NOT qualify.
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Use this skill when a driver is operating under the 150 air-mile short-haul exception and is asked to produce records. Covers the simplified time records required, when ELD is NOT required, and the documentation that satisfies inspectors.
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Use this skill to understand FMCSA cardiac certification standards. Covers what cardiac conditions disqualify, time-to-clearance, and what documentation is needed for examiner certification.
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Use this skill to track recent and upcoming SMS methodology changes from FMCSA. Covers proposed rule changes, comment periods, and implementation timelines.
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Use this skill to set proper expectations on how a DataQ challenge is actually reviewed. Covers state vs federal authority, typical timelines, and common review outcomes.
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Use this skill when the user asks about CMV operation types — Dedicated, OTR (Over-the-Road), Regional, Local, and the differences in driver lifestyle, pay, equipment, home time, hours, and customer mix. Reference industry segmentation conventions.
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Use this skill when the user asks about DataQ — FMCSA's data review system at dataqs.fmcsa.dot.gov — for disputing inspection violations, crash records, or other entries that appear in a carrier's CSA / SMS score. Covers Request for Data Review (RDR) process, success rates, common dispute grounds, what evidence to attach, timeline expectations, and how successful disputes reduce BSI (BASIC Severity Indicator) scores. Cite 49 CFR 392.7 and the FMCSA DataQs User Guide.
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