Backend

Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Use this skill when stuck in circular debugging, when solutions aren't working despite multiple attempts, or when the user expresses frustration with lack of progress. Bring in GPT-5 as a third-party consultant to provide fresh perspective on complex technical problems, architectural decisions, or multi-system debugging issues. Ideal when you've tried multiple approaches without success, when the problem involves obscure edge cases or novel challenges, or when a second expert opinion would help break through an impasse. Gather all context from the conversation so far and present it comprehensively to GPT-5.

Review code using Linus Torvalds' "good taste" philosophy. Eliminates defensive code, special cases, and deep nesting. Use when reviewing code quality, refactoring, or checking for code smells.

Download iPlug2 dependencies including plugin format SDKs (VST3, CLAP, WAM) and optional Skia graphics backend libraries

Write Ruby and Rails code in DHH's distinctive 37signals style. Use this skill when writing Ruby code, Rails applications, creating models, controllers, or any Ruby file. Triggers on Ruby/Rails code generation, refactoring requests, code review, or when the user mentions DHH, 37signals, Basecamp, HEY, or Campfire style. Embodies REST purity, fat models, thin controllers, Current attributes, Hotwire patterns, and the "clarity over cleverness" philosophy.

Write Ruby gems following Andrew Kane's proven patterns and philosophy. Use when creating new Ruby gems, refactoring existing gems, designing gem APIs, or when the user wants clean, minimal, production-ready Ruby library code. Triggers on requests like "create a gem", "write a Ruby library", "design a gem API", or mentions of Andrew Kane's style.

Generate and edit images using the Gemini API (Nano Banana Pro). Use this skill when creating images from text prompts, editing existing images, applying style transfers, generating logos with text, creating stickers, product mockups, or any image generation/manipulation task. Supports text-to-image, image editing, multi-turn refinement, and composition from multiple reference images.

Execute codeagent-wrapper for multi-backend AI code tasks. Supports Codex, Claude, and Gemini backends with file references (@syntax) and structured output.

Fast file editing via Morph Apply API (10,500 tokens/sec, 98% accuracy)