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.
plotly
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
polars
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.
pptx-posters
Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
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
High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.
pydeseq2
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.
pydicom
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
pyhealth
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
pylabrobot
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
pymc-bayesian-modeling
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
pyopenms
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
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.
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.
Just CLI
This skill should be used when the user asks to "create a justfile", "write just recipes", "configure just settings", "add just modules", "use just attributes", "set up task automation", mentions justfile, just command runner, or task automation with just.
nextjs-motion-animations
Motion-based animation system for Next.js with performance-optimized patterns
typst
Typst document creation and package development. Use when: (1) Working with .typ files, (2) User mentions typst, typst.toml, or typst-cli, (3) Creating or using Typst packages, (4) Developing document templates, (5) Converting Markdown/LaTeX to Typst
sparkbtcbot-proxy-deploy
Deploy a serverless Spark Bitcoin L2 proxy on Vercel with spending limits, auth, and Redis logging. Use when user wants to set up a new proxy, configure env vars, deploy to Vercel, or manage the proxy infrastructure.
sparkbtcbot-proxy
Use a Spark Bitcoin L2 wallet proxy for AI agents via HTTP API. Check balances, send payments, create invoices, pay L402 paywalls — all without holding the mnemonic. Use when user mentions "Spark proxy," "wallet API," "L402," "proxy payment," "bearer token auth," or wants secured Bitcoin capabilities for an agent.
sparkbtcbot
Set up Spark Bitcoin L2 wallet capabilities for AI agents. Initialize wallets from mnemonic, transfer sats and tokens, create/pay Lightning invoices, pay L402 paywalls, manage deposits and withdrawals. Use when user mentions "Spark wallet," "Spark Bitcoin," "BTKN tokens," "Spark L2," "Spark SDK," "Spark payment," "Spark transfer," "Spark invoice," "L402," "Lightning paywall," or wants Bitcoin L2 capabilities for an agent.
askme
Verbalized Sampling (VS) protocol for deep intent exploration before planning. Use when starting ambiguous or complex tasks, when multiple interpretations exist, or when you need to explore diverse intent hypotheses and ask maximum clarifying questions before committing to an approach.
ast-grep
Effective code search, analysis, and refactoring using ast-grep (sg). Use this skill for precise AST-based code modifications, structural search, and linting.
code-simplifier
Simplifies and refines code for clarity, consistency, and maintainability while preserving all functionality. Focuses on recently modified code unless instructed otherwise.
contexts
Coordinate context sweep before coding - gather relevant files, patterns, and tooling summaries. Use when preparing to implement a feature, fix, or refactor and need comprehensive architecture, pattern, tooling, and dependency context gathered first.
design-by-contract
Design-by-Contract (DbC) development - design contracts from requirements, then execute CREATE -> VERIFY -> TEST cycle. Use when implementing with formal preconditions, postconditions, and invariants using deal (Python), contracts (Rust), Zod (TypeScript), or Kotlin contracts.
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
Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.
hodd-rust
HODD-RUST validation-first Rust development - design Rust-specific verifications from requirements, then execute through validation pipeline. Use when developing Rust code with formal verification using rustfmt, clippy, static_assertions, Miri, Loom, Flux, contracts, Kani, or Lean4.
inits
Analyze a codebase and create an AGENTS.md file for future agent instances. Use when onboarding to a new repository, when the user asks to create or improve an AGENTS.md, or when documenting build/lint/test commands and high-level architecture.
outline-strong
Outline-Strong unified 5-layer validation - design all validation layers from requirements, then execute CREATE -> VERIFY -> INTEGRATE cycle. Use when implementing with comprehensive formal verification across types (Idris 2), specs (Quint), proofs (Lean 4), contracts, and tests simultaneously.
plans
Software architect and planning specialist - conduct thorough read-only planning before any action. Use when exploring a codebase to design implementation plans, defining objectives, gathering relevant files, and summarizing available tools before coding begins.
pr-reviews
Review code changes on a given GitHub PR using gh CLI. Use when the user asks to review a pull request, analyze PR diffs, or provide feedback on open PRs with structured quality, security, and testing assessments.
prompt-engineering
Interactive prompt optimization workflow for LLMs. Use when optimizing, improving, or engineering prompts for Claude, GPT, Gemini, or other language models; covers analysis, model-specific techniques, few-shot examples, XML structuring, and validation.
proof-driven
Proof-driven development with Lean 4 - design proofs from requirements, then execute CREATE -> VERIFY -> REMEDIATE cycle. Use when implementing with formal verification using Lean 4 theorems, lemmas, and proof tactics; zero-sorry policy enforced.
resolve
Resolve code review comments by verifying their validity and proposing multiple solutions for confirmed issues. Use when addressing review feedback, analyzing whether review comments are valid, and generating architectural solutions (not naive fixes) for confirmed issues.
reviews
Review the code changes on the current branch. Use when the user asks to review their current work, analyze recent commits, or get a code quality assessment of the active branch against the main branch.
srgn-cli
Practical guide for building safe, syntax-aware srgn CLI commands for source-code search and transformation. Use when users ask for srgn commands, scoped refactors (comments/docstrings/imports/functions), multi-file rewrites with --glob, custom tree-sitter query usage, or CI-style checks with --fail-any/--fail-none.
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