opentrons-integration
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
paper-2-web
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
pathml
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
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.
peer-review
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
pennylane
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
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 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.
vaex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
venue-templates
Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.
zarr-python
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
ui-ux-pro-max
UI/UX design intelligence. 50 styles, 21 palettes, 50 font pairings, 20 charts, 9 stacks (React, Next.js, Vue, Svelte, SwiftUI, React Native, Flutter, Tailwind, shadcn/ui). Actions: plan, build, create, design, implement, review, fix, improve, optimize, enhance, refactor, check UI/UX code. Projects: website, landing page, dashboard, admin panel, e-commerce, SaaS, portfolio, blog, mobile app, .html, .tsx, .vue, .svelte. Elements: button, modal, navbar, sidebar, card, table, form, chart. Styles: glassmorphism, claymorphism, minimalism, brutalism, neumorphism, bento grid, dark mode, responsive, skeuomorphism, flat design. Topics: color palette, accessibility, animation, layout, typography, font pairing, spacing, hover, shadow, gradient. Integrations: shadcn/ui MCP for component search and examples.
gh-address-comments
Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.
gh-fix-ci
Use when a user asks to debug or fix failing GitHub PR checks that run in GitHub Actions; use `gh` to inspect checks and logs, summarize failure context, draft a fix plan, and implement only after explicit approval. Treat external providers (for example Buildkite) as out of scope and report only the details URL.
imagegen
Use when the user asks to generate or edit images via the OpenAI Image API (for example: generate image, edit/inpaint/mask, background removal or replacement, transparent background, product shots, concept art, covers, or batch variants); run the bundled CLI (`scripts/image_gen.py`) and require `OPENAI_API_KEY` for live calls.
linear
Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.
notion-knowledge-capture
Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.
notion-meeting-intelligence
Prepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.
notion-research-documentation
Research across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations.
notion-spec-to-implementation
Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.
Use when tasks involve reading, creating, or reviewing PDF files where rendering and layout matter; prefer visual checks by rendering pages (Poppler) and use Python tools such as `reportlab`, `pdfplumber`, and `pypdf` for generation and extraction.
screenshot
Use when the user explicitly asks for a desktop or system screenshot (full screen, specific app or window, or a pixel region), or when tool-specific capture capabilities are unavailable and an OS-level capture is needed.
doc
Use when the task involves reading, creating, or editing `.docx` documents, especially when formatting or layout fidelity matters; prefer `python-docx` plus the bundled `scripts/render_docx.py` for visual checks.
research-lookup
Look up current research information using Perplexity 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.
uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
uniprot-database
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.
umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
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.
transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
torchdrug
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
sympy
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
backend-patterns
Backend architecture patterns, API design, database optimization, and server-side best practices for Node.js, Express, and Next.js API routes.
clickhouse-io
ClickHouse database patterns, query optimization, analytics, and data engineering best practices for high-performance analytical workloads.
coding-standards
Universal coding standards, best practices, and patterns for TypeScript, JavaScript, React, and Node.js development.
tdd-workflow
Use this skill when writing new features, fixing bugs, or refactoring code. Enforces test-driven development with 80%+ coverage including unit, integration, and E2E tests.
algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
brand-guidelines
Applies Anthropic's official brand colors and typography to any sort of artifact that may benefit from having Anthropic's look-and-feel. Use it when brand colors or style guidelines, visual formatting, or company design standards apply.
canvas-design
Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create original visual designs, never copying existing artists' work to avoid copyright violations.
doc-coauthoring
Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This workflow helps users efficiently transfer context, refine content through iteration, and verify the doc works for readers. Trigger when user mentions writing docs, creating proposals, drafting specs, or similar documentation tasks.
frontend-design
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications (examples include websites, landing pages, dashboards, React components, HTML/CSS layouts, or when styling/beautifying any web UI). Generates creative, polished code and UI design that avoids generic AI aesthetics.
internal-comms
A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use this skill whenever asked to write some sort of internal communications (status reports, leadership updates, 3P updates, company newsletters, FAQs, incident reports, project updates, etc.).
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
pytorch-lightning
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
qiskit
IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
research-grants
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
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