triton-kernel-writing
triton-kernel-writing
Write or review Triton kernels for vLLM, with practical guidance for generated-code inspection, launch grids, indexing, specialization, tuning, and representative performance validation.
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genomic-coordinates
genomic-coordinates
Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region…
pathway-enrichment
pathway-enrichment
Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enri…
torchdrug
torchdrug
Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and knowledge graph reasoning. Use when code imports torchdrug or needs its datasets, models, tasks, or Engine.
sql-optimization-patterns
sql-optimization-patterns
Diagnose slow SQL with query plans, preserve query results, and verify indexing or query changes against representative data.
voice-agents
voice-agents
Voice agents represent the frontier of AI interaction - humans speaking naturally with AI systems.
poka-yoke
poka-yoke
Mistake-proof code so misuse cannot be expressed, rather than warning against it. Use when designing an interface, schema, or state machine and the user wants it hard to get wrong ("make invalid states unrepresentable", "so callers cannot screw it up", "type-safe API", "pit of success"); when auditing existing code for footguns ("what could bite us here", "…
sparse-autoencoder-training
sparse-autoencoder-training
Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.
scgpt
scgpt
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use…
algorithm-visualizer
algorithm-visualizer
Generate visual representations of algorithm execution
graph-modeler
graph-modeler
Convert problem descriptions into graph representations
decision-visualization
decision-visualization
Decision-specific visualization skill for creating clear, actionable visual representations of analyses
supply-chain-digital-twin
supply-chain-digital-twin
Digital twin representation of supply chain for real-time monitoring and simulation
stakeholder-facilitation
stakeholder-facilitation
Facilitate meetings, workshops, and community consultations with diverse stakeholders including artists, board members, funders, and community representatives
tooluniverse-microbial-genome-characterization
tooluniverse-microbial-genome-characterization
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enum…
tooluniverse-microbial-genome-characterization
tooluniverse-microbial-genome-characterization
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enum…
tooluniverse-neurosynth-meta-analysis
tooluniverse-neurosynth-meta-analysis
Meta-analytic decoding of human fMRI coordinates using the Neurosynth coordinate database (14,371 studies, ~3,228 cognitive/neuroscience terms) — given an MNI brain coordinate, statistically identify which cognitive terms are over-represented in studies reporting activation there ("reverse inference"); given a term, find the studies and coordinates most ass…
tooluniverse-fastq-qc
tooluniverse-fastq-qc
FASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, interpret per-base sequence quality, per-base N content, adapter content, overrepresented sequences, sequence duplication and GC content, and decide whether (and how) to trim with fastp / Cutadapt before downstream a…
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