tdd-cycle
执行 TDD 红绿重构循环（RED→GREEN→REFACTOR→REPEAT），通过先写失败测试、最小代码实现、保持绿色重构的节奏驱动开发。当启动功能开发、需要测试驱动节奏、进行迭代编码、追求高测试覆盖率时使用。提供检查清单和节奏控制。
interview-to-us
将访谈记录、会议纪要、邮件沟通等非结构化内容快速转换为符合CRAFT标准的User Story草稿。适合在需求调研阶段使用，当有大量访谈笔记需要结构化时。帮助不会写US的PM/BA快速上手，从自然语言访谈记录自动提取As-Want-So结构，节省手动整理时间（1小时→10分钟）。
tech-selection-explain
将技术选型决策转换为业务语言解释，生成客户友好的技术说明。当ARCH中技术术语过多、需要向PM/客户解释时使用。
vs-coverage-check
检查每个US是否有对应的VS，生成覆盖率报告和修复建议。当设计文档创建后、CONSTRAINT验收前使用，避免US→VS覆盖率<100%导致验收失败。
goal-granularity-check
确保GOAL粒度合理，不过粗或过细。当GOAL创建完成后使用，确保GOAL符合单一职责原则。
principle-soc
实现关注点分离，确保不同职责模块化和边界清晰。当需要架构分层设计、模块职责划分、横切关注点处理时使用。覆盖层次分离、功能分离、横切关注点三大维度，提供分离检查清单和耦合问题的诊断修复方法。
principle-kiss
保持设计和实现的简单性，识别并消除不必要的复杂度。当需要架构设计评审、代码简化重构、接口设计优化时使用。覆盖代码、架构、接口、流程四大维度，提供简单性检查清单和过度复杂性的诊断修复方法。
web-app-thinking
提供网页应用全栈架构思考框架，涵盖前端渲染策略、后端 API 设计、基础设施部署、安全防护、性能优化五大维度。当需要设计完整 Web 应用、评审网页系统架构、或需要全局视角审视前后端协同设计时使用。支持 SPA/MPA、SSR/CSR、REST/GraphQL、容器/Serverless 等多种技术栈决策。
arch-options-compare
比较多个架构方案（单体/微服务等），从SOLID原则、成本、复杂度等维度评分，生成对比表和推荐方案。当需要向客户解释架构选择或ADR决策时使用。
pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
medical-newsletter-writer
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parallel-literature-search
Parallel search across PubMed, Perplexity, and your knowledge base. Searches all sources simultaneously and synthesizes findings with citations. Faster evidence gathering for clinical questions.
cardiology-science-for-people
Write rigorous, accurate cardiology science for general audiences—not doctors. Use when the user wants to: (1) Explain clinical trials or research in plain English, (2) Write science content an 8th grader can understand WITHOUT dumbing it down, (3) Create thought leadership for the intelligent public rather than medical peers, (4) Transform complex cardiology findings into stories and narratives, (5) Write pieces where readers DON'T need another LLM to understand the explanation. Maintains full scientific rigor with PubMed citations for verification while avoiding academic language, trial acronyms, and intimidating statistics.
hypogenic
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
perplexity-search
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's 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.
quick-topic-researcher
Rapid topic mastery for video/content prep. Takes a topic → generates 5 research questions → parallel PubMed + web search → outputs McKinsey-style brief in 5 minutes. Use BEFORE recording videos or writing content.
qiskit
Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.
research-grants
Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
research-lookup
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
pylabrobot
Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR, Opentrons OT-2, Tecan EVO), integrating lab equipment, managing deck layouts and resources (plates, tips, containers), reading plates, or creating reproducible laboratory protocols. Applicable for both simulated protocols and physical hardware control.
deep-researcher
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources. Uses file-based research tracking, parallel investigation threads, and context-efficient patterns for deep investigations. ALL MEDICAL CITATIONS FROM PUBMED MCP ONLY.
treatment-plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
cardiology-youtube-scriptwriter
End-to-end YouTube content creation for cardiology channels. Use when user wants to create YouTube videos about cardiology, heart health, or cardiovascular topics. Triggers on greetings with content intent, requests for video ideas or scripts, help with cardiology YouTube channels, heart health video content requests, or any cardiology content creation conversation. Handles complete workflow from ideation through social listening, topic selection, and full script delivery.
academic-chapter-writer
Comprehensive academic textbook chapter writing system for medical/scientific content. Use when the user wants to: (1) Write a full textbook chapter (5,000-15,000 words) on any medical/scientific topic, (2) Generate a detailed table of contents with section word counts, (3) Research topics via PubMed MCP and compile 20-30 references, (4) Write section-by-section with proper citations in Vancouver format, (5) Create publishable academic content with Eric Topol-inspired voice and authentic human prose, (6) Get approval at TOC stage before writing begins, (7) Export well-structured chapters for textbook publication.
biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
ena-database
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.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
esm
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.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
flowio
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.
pathml
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
pennylane
Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables building and training quantum circuits with automatic differentiation, seamless integration with PyTorch/JAX/TensorFlow, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ, etc.). Use when working with quantum circuits, variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, molecular simulations, quantum chemistry calculations, or any quantum computing tasks requiring gradient-based optimization, hardware-agnostic programming, or quantum machine learning workflows.
plotly
Interactive scientific and statistical data visualization library for Python. Use when creating charts, plots, or visualizations including scatter plots, line charts, bar charts, heatmaps, 3D plots, geographic maps, statistical distributions, financial charts, and dashboards. Supports both quick visualizations (Plotly Express) and fine-grained customization (graph objects). Outputs interactive HTML or static images (PNG, PDF, SVG).
polars
Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows.
protocolsio-integration
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 and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
pubmed-database
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
pufferlib
This skill should be used when working with reinforcement learning tasks including high-performance RL training, custom environment development, vectorized parallel simulation, multi-agent systems, or integration with existing RL environments (Gymnasium, PettingZoo, Atari, Procgen, etc.). Use this skill for implementing PPO training, creating PufferEnv environments, optimizing RL performance, or developing policies with CNNs/LSTMs.
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