Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets,...
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard),...
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps...
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate...
Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), creating custom Gym environments, implementing callbacks for monitoring and...
Use when errors occur deep in execution and you need to trace back to find the original trigger - systematically traces bugs backward through call stack, adding instrumentation when needed, to...
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
Analyze datasets to discover patterns, anomalies, and relationships. Use when exploring data files, generating statistical summaries, checking data quality, or creating visualizations. Supports...
Executes OpenAI Codex CLI for code analysis, refactoring, and automated editing. Activates when users mention codex commands, code review requests, or automated code transformations requiring...
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
Use when writing or changing tests, adding mocks, or tempted to add test-only methods to production code - prevents testing mock behavior, production pollution with test-only methods, and mocking...
Automatically generates comprehensive test suites (unit, integration, E2E) based on code and past testing patterns. Use when user says "write tests", "test this", "add coverage", or after fixing...
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML...
Use when complex problems require systematic step-by-step reasoning with ability to revise thoughts, branch into alternative approaches, or dynamically adjust scope. Ideal for multi-stage...
Use when executing implementation plans with independent tasks in the current session - dispatches fresh subagent for each task with code review between tasks, enabling fast iteration with quality gates
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