Results for “benchmark”

Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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Extract typical annual GPP, annual evapotranspiration, mid-season LAI, mid-season root biomass, mid-season shoot biomass, median canopy height, maximum primary-root depth, Vcmax at 25oC, and Jmax at 25oC from EcoSIM h0 NetCDF output files. Use when asked to derive these EcoSIM output targets from a selected .ecosim.h0.*.nc file for model-output processing, trait checks, or benchmark summaries.

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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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Achieve aggressive v3 performance targets: 2.49x-7.47x Flash Attention speedup, 150x-12,500x search improvements, 50-75% memory reduction. Comprehensive benchmarking and optimization suite.

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Interactive developer experience plan review. Explores developer personas, benchmarks against competitors, designs magical moments, and traces friction points before scoring. Three modes: DX EXPANSION (competitive advantage), DX POLISH (bulletproof every touchpoint), DX TRIAGE (critical gaps only). Use when asked to "DX review", "developer experience audit", "devex review", or "API design review". Proactively suggest when the user has a plan for developer-facing products (APIs, CLIs, SDKs, libraries, platforms, docs). (gstack) Voice triggers (speech-to-text aliases): "dx review", "developer experience review", "devex review", "devex audit", "API design review", "onboarding review".

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Guides Rust performance optimization. Use when profiling, benchmarking, reducing allocations, improving cache locality, choosing between rayon/async/threads, or applying SIMD/parallelism.

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Show ponytail's measured impact as a compact scoreboard: less code, less cost, more speed, from the benchmark medians. One-shot display, not a persistent mode, and not a per-repo number. Trigger: /ponytail-gain, "ponytail gain", "what does ponytail save", "show ponytail impact", "ponytail scoreboard".

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You're a quality engineer who has seen agents that aced benchmarks fail spectacularly in production. You've learned that evaluating LLM agents is fundamentally different from testing traditional software—the same input can produce different outputs, and "correct" often has no single answer.

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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Use this skill when the user asks about trucking rate negotiation — cost-plus pricing, market rate benchmarking via DAT/Truckstop, fuel surcharge math, how to negotiate with brokers/shippers, when to walk away, contract pricing vs spot rates. Reference DAT Rate Analytics + freight market reports.

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Use when a carrier asks how to improve MPG, lower fuel cost per mile, manage fuel surcharge, set up a fuel-purchase strategy (in-network vs out-of-network), train drivers on fuel-efficient driving, spec new tractors for fuel economy, or benchmark fleet MPG against industry averages.

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Use when adding or repairing Spark regression tests for asynchronous ownership, cancellation, persistence, restart recovery, or cross-surface projections. Not a coverage campaign, performance benchmark, source-text policy check, or full delivery review.

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Find the cheapest AI model that is smart enough for a task, and the cheapest provider to run it on, from live Artificial Analysis benchmarks via Firecrawl. Use when the user asks which model to use, how to cut their LLM or API bill, whether a cheaper model would do, which provider is cheapest or fastest for a model, which open-weights model to self-host, or wants something built with the cheapest model for each step.

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Use when adding or repairing Spark regression tests for asynchronous ownership, cancellation, persistence, restart recovery, or cross-surface projections. Not a coverage campaign, performance benchmark, source-text policy check, or full delivery review.

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Go testing patterns including table-driven tests, subtests, benchmarks, fuzzing, and test coverage. Follows TDD methodology with idiomatic Go practices.

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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, update or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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Apply systematic performance optimization techniques when writing or reviewing code. Use when optimizing hot paths, reducing latency, improving throughput, fixing performance regressions, or when the user mentions performance, optimization, speed, latency, throughput, profiling, or benchmarking.

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Scan global talent markets via GitHub/Arxiv/LinkedIn APIs, build talent heatmaps with salary benchmarks, identify Tier S/A/B/C candidates. Use when: quarterly talent scanning, critical role hiring, competitive intelligence on talent pools. Includes real API integrations and data pipeline.

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Design irresistible offer packages with real salary benchmarks, negotiation playbooks, and competitive counter-strategies. Co-designed with Siku (司库). Includes total compensation calculator, negotiation scripts, and BATNA analysis.

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Test and assure quality — test plan, QA, coverage, unit test, integration test, end-to-end, performance, benchmark, regression. Applies TDD and FIRST principles for the CTO office's tester.

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Set up eval-based QA for Python LLM applications: instrument the app, build golden datasets, write and run eval tests, and iterate on failures. ALWAYS USE THIS SKILL when the user asks to set up QA, add tests, add evals, evaluate, benchmark, fix wrong behaviors, improve quality, or do quality assurance for any Python project that calls an LLM model.

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