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Avalia LLMs em 100+ benchmarks de 18+ harnesses (MMLU, HumanEval, GSM8K, segurança, VLM) com execução multi-backend. Use quando precisar de avaliação escalável em Docker local, HPC Slurm ou plataformas cloud. Plataforma enterprise-grade da NVIDIA com arquitetura container-first para benchmarking reproduzível.
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Distributed machine learning, data mining, and iterative HPC with Exasol. Covers end-to-end ML pipelines (DISTRIBUTE BY + SET scripts + BucketFS), per-entity federated training with partial_fit and ctx.reset(), batch inference, map-reduce ensemble training, distributed ensemble and SON algorithm for frequent itemset mining (Apriori, FP-Growth, association rules, market-basket analysis), Lua execute script orchestration for iterative algorithms (k-means, SGD, gradient descent), scikit-learn model training, parallel hyperparameter search, per-entity forecasting, anomaly detection, model lifecycle in BucketFS (pickle/joblib/ONNX versioning), GPU acceleration via CUDA SLCs (PyTorch/TensorFlow/RAPIDS), and ML-specific performance tuning (skew, OOM, multi-pass chunking).
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End-to-end playbook for creating a new NV oOS Pro toolkit under addons/pro/includes/tools/<toolkit> — folder layout, service layer, tool class conventions (canonical envelope, two-gate sanitisation, capability flags), ALL eleven registration surfaces (Pro module registry loader, central registry, admin Tools section + Features subtab, admin settings page/side menu, settings status map, both WP-CLI commands, schedule presets, workflow presets, SA Toolkit Manager, coverage manifests), fixture/oracle testing with a standalone smoke harness, and the phpcs gotcha checklist. Use when asked to build a new Pro toolkit, add a toolkit to the plugin, scaffold toolkit tools, register toolkit presets/toggles, or debug why a new toolkit's tools, toggle, or admin menu don't appear. First case study: food-beverage (F&B Management, 21 tools, 2026-10-08, 20/20 Check-totals oracle verified). Complements mcp-ai-wpoos-toolkit-audit (hardening existing toolkits) and mcp-ai-wpoos-test-suite (repair).
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Per-toolkit hardening audit loop for NV oOS Pro tools. Systematically scans each addons/pro/includes/tools/<toolkit> (and its plugins/nvoos-content-graph-pro mirror) for the recurring production failure classes — unguarded shell calls that fatal on exec-disabled hosts, calls to nonexistent client methods, string-assuming parsing of provider responses that may be arrays, provider enum/service mismatches, metric/source column drift that silently returns 0, secondary-table denominator gaps, the Chart.js fixed-height loop, misleading native-source errors, and silent import truncation that reports partial writes as success — then fixes, tests (Docker PHPUnit), and validates (phpcs both standards) before moving to the next toolkit. Use when asked to audit a toolkit, review the X tools for similar issues, do the same for the other toolkits, or continue the toolkit audit loop. The first case study (document-generation) found 3 fatal bugs + 1 broken regex; the food-beverage pass added classes 5–9.
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Azure Batch SDK for Java. Run large-scale parallel and HPC batch jobs with pools, jobs, tasks, and compute nodes.
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Azure Batch SDK for Java. Run large-scale parallel and HPC batch jobs with pools, jobs, tasks, and compute nodes.
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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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Evaluates LLMs across 100+ benchmarks from 18+ harnesses (MMLU, HumanEval, GSM8K, safety, VLM) with multi-backend execution. Use when needing scalable evaluation on local Docker, Slurm HPC, or cloud platforms. NVIDIA's enterprise-grade platform with container-first architecture for reproducible benchmarking.
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Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.
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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.
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Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.
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Azure Batch SDK for Java. Run large-scale parallel and HPC batch jobs with pools, jobs, tasks, and compute nodes.
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Azure Batch SDK for Java. Run large-scale parallel and HPC batch jobs with pools, jobs, tasks, and compute nodes.
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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.
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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.
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Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.
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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.
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Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.
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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.
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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.
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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.
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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.
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Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic Hi-C loop callers (cooltools dots, Juicer HiCCUPS) use the wrong null. Covers FitHiChIP (config-driven coverage+distance-decay spline regression, peak-to-peak vs peak-to-all foreground, loose vs stringent background, coverage vs ICE bias), MAPS (positive Poisson regression on bias factors for PLAC-seq/HiChIP), hichipper (restriction-site-distance bias model + library QC), CHiCAGO (Delaporte two-component Brownian+technical background for asymmetric bait x other-end Capture Hi-C), the with/without separate-ChIP anchor decision, and differential loops via diffloop. Use when calling loops from HiChIP/PLAC-seq/Capture Hi-C, choosing FitHiChIP/MAPS/CHiCAGO, picking peak-to-all vs peak-to-peak, setting the loop FDR, supplying ChIP peaks as anchors, QCing a HiChIP library, or comparing loops between conditions.
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Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.
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