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Create diverse synthetic test inputs for LLM pipeline evaluation using dimension-based tuple generation. Use when bootstrapping an eval dataset, when real user data is sparse, or when stress-testing specific failure hypotheses. Do NOT use when you already have 100+ representative real traces (use stratified sampling instead), or when the task is collecting production logs.
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Specify the tracing, metrics, and alerting for an AI agent or LLM feature in production. Use when asked what to log for an LLM app, design agent tracing or spans, define quality and cost monitors, or answer 'how do we know if the agent is misbehaving?'. Produces an observability spec with a trace schema, metric definitions with owners and alert thresholds, sampling and retention policy, and a privacy note for logged content.
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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.
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Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitoring, treating MRD as a binary integrated detection call across the patient's full variant set (with a defined LoD95 and per-sample specificity) rather than a per-timepoint VAF threshold, and handling undetectable samples as left-censored at the per-sample limit of detection rather than true zeros. Covers tumor-informed bespoke vs tumor-naive design, landmark vs surveillance sampling, molecular-response definitions and their non-standardization, censoring-aware clearance kinetics, and the multiple-testing structure of repeated surveillance. Use when monitoring ctDNA during therapy, calling molecular relapse before imaging, or estimating clearance half-life from serial samples.
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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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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).
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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.
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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.
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Best-practices reference for preparing and instrumenting applications on Temps. Covers the app runtime contract (`.temps.yaml` health, HOST/PORT, readiness, SIGTERM, replicas, migrations) and production observability (errors, traces, metrics, logs, analytics, privacy, sampling, cardinality, credential boundaries). Use whenever building or reviewing an app for Temps, configuring health checks, adding telemetry, diagnosing missing/noisy signals, or checking OTLP/Sentry/analytics ingestion. Triggers include "temps best practices", "prepare this app for Temps", ".temps.yaml health", "temps health check", "ignore health checks in otel", "temps observability", "wire up telemetry", and "instrument this app for temps". Prefer focused setup skills for a single SDK. Use temps-cli for executing deploy and resource-management commands.
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This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, an
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A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.
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Expert knowledge for Azure Microsoft Opentelemetry development including configuration. Use when setting sampling, exporters, resource attributes, env vars, or tuning tracing/metrics behavior, and other Azure Microsoft Opentelemetry related development tasks. Not for Azure Monitor (use azure-monitor).
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OpenTelemetry setup, span context propagation, sampling strategies, Jaeger queries
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Time-series database implementation for metrics, IoT, financial data, and observability backends. Use when building dashboards, monitoring systems, IoT platforms, or financial applications. Covers TimescaleDB (PostgreSQL), InfluxDB, ClickHouse, QuestDB, continuous aggregates, downsampling (LTTB), and retention policies.
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Use when you need to implement or improve distributed tracing with OpenTelemetry in Java — including trace/span modeling, context propagation, semantic conventions, span attributes/events/status, sampling strategy, baggage usage, privacy safeguards, and backend integration with OTLP collectors. This should trigger for requests such as Improve tracing; Apply OpenTelemetry tracing; Add distributed tracing; Refactor tracing instrumentation; Instrument Java services with OpenTelemetry spans. Part of Plinth Toolkit
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Market data preparation including OHLCV resampling, gap handling, anomaly detection, normalization, and multi-source merging
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Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
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Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.
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PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet), social/knowledge graphs, 3D point clouds. For non-graph DL use PyTorch; for classical graph algorithms use NetworkX.
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Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
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Blender rendering with Cycles and Eevee including sampling, denoising, camera setup, render passes, color management, and render optimization. Use for final output and look validation via MCP.
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Use DPM-Solver and DPM-Solver++ single-file samplers for diffusion ODE sampling, PyTorch/JAX integration, ScoreSDE/DDPM examples, and Stable Diffusion acceleration.
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Use audio-diffusion-pytorch for PyTorch waveform diffusion generators, text-conditioned audio generation, inpainting, upsampling, vocoding, and diffusion autoencoding.
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Guides CUDA-based BigGAN-PyTorch training, checkpoint sampling, dataset preparation, metric preparation, model customization, and optional TensorFlow Hub weight conversion.
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