# Scientific Skills

## Scientific Databases & Data Access

- **Database Lookup** - Search 78 public scientific, biomedical, materials science, and economic databases via their REST APIs and return structured JSON results. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD, Exoplanet Archive), earth/environment (USGS, NOAA, EPA, OpenWeatherMap), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, DailyMed, ZINC, BindingDB), materials science (Materials Project, COD), biology/genomics (Reactome, BRENDA, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, ChEBI, BioGRID, Gene Ontology, QuickGO, NCBI Protein/Taxonomy, dbSNP, SRA, ENA, gnomAD, UCSC Genome, ENCODE, JASPAR, MouseMine, PRIDE, LINCS L1000, Human Protein Atlas, Human Cell Atlas, RummaGEO, Metabolomics Workbench, EMDB, Addgene), disease/clinical (COSMIC, Open Targets, ClinPGx, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog, Monarch, HPO), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, BEA, BLS, Federal Reserve, World Bank, ECB, US Treasury, Alpha Vantage, Data Commons), and demographics (US Census, Eurostat, WHO). Use this skill whenever the user wants to look up compounds, drugs, proteins, genes, pathways, enzymes, gene expression, variants, clinical trials, patents, SEC filings, economic indicators, crystal structures, astronomical objects, earthquakes, weather, or any data from a public database API
- **DepMap** - Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets
- **Imaging Data Commons** - Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses
- **PrimeKG** - Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more. Integrates 20+ biomedical resources into a single knowledge graph for drug repurposing, disease mechanism exploration, and target identification
- **U.S. Treasury Fiscal Data** - Free, open REST API from the U.S. Department of the Treasury providing 54 datasets and 179 data tables covering federal fiscal data. No API key required. Access national debt (Debt to the Penny back to 1993, Historical Debt back to 1790), Daily Treasury Statements (TGA balances, deposits/withdrawals), Monthly Treasury Statements (federal budget receipts and outlays), Treasury securities auctions data (bills, notes, bonds, TIPS, FRNs since 1979), average interest rates on Treasury securities, Treasury reporting exchange rates (quarterly for 170+ currencies), I Bond and savings bond rates, TIPS/CPI data, and more. Supports filtering, sorting, pagination, and CSV/XML/JSON output formats
- **Hugging Science** - Curated, LLM-friendly catalog of scientific datasets, models, blog posts, and interactive Spaces hosted on Hugging Face, spanning 17 scientific domains (astronomy, benchmark, biology, biotechnology, chemistry, climate, conservation, earth-science, ecology, energy, engineering, genomics, materials-science, mathematics, medicine, physics, scientific-reasoning). Discovery happens via huggingscience.co (with `llms.txt`, `llms-full.txt`, and per-topic markdown files designed for agent consumption); usage goes through standard Hugging Face APIs. Includes a bundled `fetch_catalog.py` script for filtered access by topic, type (datasets/models/blogs/spaces), or free-text search, plus reference guides for loading datasets via the `datasets` library (with streaming for billion-token corpora), running models via `transformers` or the Inference API/Providers (handling `trust_remote_code` requirements for custom architectures like Evo-2), and calling Spaces via `gradio_client` (with a worked BoltzGen example for protein binder design). Authenticates gated resources via `HF_TOKEN` from `.env`. Use cases: discovering the right dataset/model for a scientific ML task without trawling the broader Hub, fine-tuning on curated scientific data, citing methodology blogs from dataset/model authors, running interactive scientific demos (binder design, theorem proving, weather modeling) without local GPU setup, and bridging from "I need a model for protein/genome/molecule/climate/materials/astronomy" to working code

## Scientific Integrations

### Laboratory Information Management Systems (LIMS) & R&D Platforms
- **Benchling Integration** - Toolkit for integrating with Benchling's R&D platform, providing programmatic access to laboratory data management including registry entities (DNA sequences, proteins), inventory systems (samples, containers, locations), electronic lab notebooks (entries, protocols), workflows (tasks, automation), and data exports using Python SDK and REST API

### Cloud Platforms for Genomics & Biomedical Data
- **DNAnexus Integration** - Comprehensive toolkit for working with the DNAnexus cloud platform for genomics and biomedical data analysis. Covers building and deploying apps/applets (Python/Bash), managing data objects (files, records, databases), running analyses and workflows, using the dxpy Python SDK, and configuring app metadata and dependencies (dxapp.json setup, system packages, Docker, assets). Enables processing of FASTQ/BAM/VCF files, bioinformatics pipelines, job execution, workflow orchestration, and platform operations including project management and permissions

### Laboratory Automation
- **Opentrons Integration** - Toolkit for creating, editing, and debugging Opentrons Python Protocol API v2 protocols for laboratory automation using Flex and OT-2 robots. Enables automated liquid handling, pipetting workflows, hardware module control (thermocycler, temperature, magnetic, heater-shaker, absorbance plate reader), labware management, and complex protocol development for biological and chemical experiments
- **Ginkgo Cloud Lab** - Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Supports three protocols: Cell Free Protein Expression Validation ($39/sample, 5-10 day turnaround), Cell Free Protein Expression Optimization ($199/sample, DoE across 24 conditions, 6-11 days), and Fluorescent Pixel Art Generation ($25/plate, bacterial artwork with 11 fluorescent E. coli strains, 5-7 days). Includes EstiMate AI agent for custom protocol feasibility and pricing

### Electronic Lab Notebooks (ELN)
- **LabArchives Integration** - Toolkit for interacting with LabArchives Electronic Lab Notebook (ELN) REST API. Provides programmatic access to notebooks (backup, retrieval, management), entries (creation, comments, attachments), user authentication, site reports and analytics, and third-party integrations (Protocols.io, GraphPad Prism, SnapGene, Geneious, Jupyter, REDCap). Includes Python scripts for configuration setup, notebook operations, and entry management. Supports multi-regional API endpoints (US, UK, Australia) and OAuth authentication
- **Open Notebook** - Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Organizes research materials into notebooks, ingests diverse content sources (PDFs, videos, audio, web pages, Office documents), generates AI-powered notes and summaries, creates multi-speaker podcasts from research, enables document chat with context-aware AI, and searches across materials with full-text and vector search. Supports 16+ AI providers including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral with complete data privacy through self-hosting

### Workflow Platforms & Cloud Execution
- **LatchBio Integration** - Integration with the Latch platform for building, deploying, and executing bioinformatics workflows. Provides comprehensive support for creating serverless bioinformatics pipelines using Python decorators, deploying Nextflow/Snakemake pipelines, managing cloud data (LatchFile, LatchDir) and structured Registry (Projects, Tables, Records), configuring computational resources (CPU, GPU, memory, storage), and using pre-built Latch Verified workflows (RNA-seq, AlphaFold, DESeq2, single-cell analysis, CRISPR editing). Enables automatic containerization, UI generation, workflow versioning, and execution on scalable cloud infrastructure with comprehensive data management

### Microscopy & Bio-image Data
- **OMERO Integration** - Toolkit for interacting with OMERO microscopy data management systems using Python. Provides comprehensive access to microscopy images stored in OMERO servers, including dataset and screening data retrieval, pixel data analysis, annotation and metadata management, regions of interest (ROIs) creation and analysis, batch processing, OMERO.scripts development, and OMERO.tables for structured data storage. Essential for researchers working with high-content screening data, multi-dimensional microscopy datasets, or collaborative image repositories

### Protocol Management & Sharing
- **Protocols.io Integration** - Integration with protocols.io API for managing scientific protocols. Enables programmatic access to protocol discovery (search by keywords, DOI, category), protocol lifecycle management (create, update, publish with DOI), step-by-step procedure documentation, collaborative development with workspaces and discussions, file management (upload data, images, documents), experiment tracking and documentation, and data export. Supports OAuth authentication, protocol PDF generation, materials management, threaded comments, workspace permissions, and institutional protocol repositories. Essential for protocol standardization, reproducibility, lab knowledge management, and scientific collaboration

## Scientific Packages

### Bioinformatics & Genomics
- **AnnData** - Python package for handling annotated data matrices, specifically designed for single-cell genomics data. Provides efficient storage and manipulation of high-dimensional data with associated annotations (observations/cells and variables/genes). Key features include: HDF5-based h5ad file format for efficient I/O and compression, integration with pandas DataFrames for metadata, support for sparse matrices (scipy.sparse) for memory efficiency, layered data organization (X for main data matrix, obs for observation annotations, var for variable annotations, obsm/varm for multi-dimensional annotations, obsp/varp for pairwise matrices), and seamless integration with Scanpy, scvi-tools, and other single-cell analysis packages. Supports lazy loading, chunked operations, and conversion to/from other formats (CSV, HDF5, Zarr). Use cases: single-cell RNA-seq data management, multi-modal single-cell data (RNA+ATAC, CITE-seq), spatial transcriptomics, and any high-dimensional annotated data requiring efficient storage and manipulation
- **Arboreto** - Scalable Python GRN inference (Aerts Lab) using GRNBoost2 (gradient boosting) and GENIE3 (random forest) with Dask distributed execution. Accepts pandas DataFrames, dense NumPy arrays, or sparse CSC matrices (cells × genes). Features: local multi-core and cluster scheduling, TF-restricted search, `limit` for top-N links, and `diy()` for custom regressors. Core engine for pySCENIC (cisTarget pruning and regulon activity are downstream). Use for bulk or single-cell expression matrices when inferring TF–target regulatory links from co-expression patterns
- **BioPython** - Comprehensive Python library for computational biology and bioinformatics providing tools for sequence manipulation, database access, and biological data analysis. Key features include: sequence objects (Seq, SeqRecord, SeqIO) for DNA/RNA/protein sequences with biological alphabet validation, file format parsers (FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, PDB, SAM/BAM, VCF, GFF), NCBI database access (Entrez Programming Utilities for PubMed, GenBank, BLAST, taxonomy), BLAST integration (running searches, parsing results), sequence alignment (pairwise and multiple sequence alignment with Bio.Align), phylogenetics (tree construction and manipulation with Bio.Phylo), population genetics (Hardy-Weinberg, F-statistics), protein structure analysis (PDB parsing, structure calculations), and statistical analysis tools. Supports integration with NumPy, pandas, and other scientific Python libraries. Use cases: sequence analysis, database queries, phylogenetic analysis, sequence alignment, file format conversion, and general bioinformatics workflows
- **BioServices** - Python library providing unified programmatic access to 40+ biological web services and databases. Supports major bioinformatics resources including KEGG (pathway and compound data), UniProt (protein sequences and annotations), ChEBI (chemical entities), ChEMBL (bioactive molecules), Reactome (pathways), IntAct (protein interactions), BioModels (biological models), and many others. Features consistent API across different services, automatic result caching, error handling and retry logic, support for both REST and SOAP web services, and conversion of results to Python objects (dictionaries, lists, BioPython objects). Handles authentication, rate limiting, and API versioning. Use cases: automated data retrieval from multiple biological databases, building bioinformatics pipelines, database integration workflows, and programmatic access to biological web resources without manual web browsing
- **Cellxgene Census** - Python package for querying and analyzing large-scale single-cell RNA-seq data from the CZ CELLxGENE Discover census. Provides access to 50M+ cells across 1,000+ datasets with standardized annotations and metadata. Key features include: efficient data access using TileDB-SOMA format for scalable queries, integration with AnnData and Scanpy for downstream analysis, cell metadata filtering and querying, gene expression retrieval, and support for both human and mouse data. Enables subsetting datasets by cell type, tissue, disease, or other metadata before downloading, reducing data transfer and memory requirements. Supports local caching and batch operations. Use cases: large-scale single-cell analysis, cell-type discovery, cross-dataset comparisons, reference dataset construction, and exploratory analysis of public single-cell data
- **deepTools** - Comprehensive suite of Python tools for exploring and visualizing next-generation sequencing (NGS) data, particularly ChIP-seq, RNA-seq, and ATAC-seq experiments. Provides command-line tools and Python API for processing BAM and bigWig files. Key features include: quality control metrics (plotFingerprint, plotCorrelation), coverage track generation (bamCoverage for creating bigWig files), matrix generation for heatmaps (computeMatrix, plotHeatmap, plotProfile), comparative analysis (multiBigwigSummary, plotPCA), and efficient handling of large files. Supports normalization methods, binning options, and various visualization outputs. Designed for high-throughput analysis workflows and publication-quality figure generation. Use cases: ChIP-seq peak visualization, RNA-seq coverage analysis, ATAC-seq signal tracks, comparative genomics, and NGS data exploration
- **FlowIO** - Python library for reading and manipulating Flow Cytometry Standard (FCS) files, the standard format for flow cytometry data. Provides efficient parsing of FCS files (versions 2.0, 3.0, 3.1), access to event data (fluorescence intensities, scatter parameters), metadata extraction (keywords, parameters, acquisition settings), and conversion to pandas DataFrames or NumPy arrays. Features include: support for large FCS files, handling of multiple data segments, access to text segments and analysis segments, and integration with flow cytometry analysis workflows. Enables programmatic access to flow cytometry data for downstream analysis, visualization, and machine learning applications. Use cases: flow cytometry data analysis, high-throughput screening, immune cell profiling, and automated processing of FCS files
- **gget** - Command-line tool and Python package for efficient querying of genomic databases with a simple, unified interface. Provides fast access to Ensembl (gene information, sequences, orthologs, variants), UniProt (protein sequences and annotations), NCBI (BLAST searches, gene information), PDB (protein structures), COSMIC (cancer mutations), and other databases. Features include: single-command queries without complex API setup, automatic result formatting, batch query support, integration with pandas DataFrames, and support for both command-line and Python API usage. Optimized for speed and ease of use, making database queries accessible to users without extensive bioinformatics experience. Use cases: quick gene lookups, sequence retrieval, variant annotation, protein structure access, and rapid database queries in bioinformatics workflows
- **geniml** - Genomic interval machine learning toolkit providing unsupervised methods for building ML models on BED files. Key capabilities include Region2Vec (word2vec-style embeddings of genomic regions and region sets using tokenization and neural language modeling), BEDspace (joint embeddings of regions and metadata labels using StarSpace for cross-modal queries), scEmbed (Region2Vec applied to single-cell ATAC-seq data generating cell-level embeddings for clustering and annotation with scanpy integration), consensus peak building (four statistical methods CC/CCF/ML/HMM for creating reference universes from BED collections), and comprehensive utilities (BBClient for BED caching, BEDshift for genomic randomization preserving context, evaluation metrics for embedding quality, Text2BedNN for neural search backends). Part of BEDbase ecosystem. Supports Python API and CLI workflows, pre-trained models on Hugging Face, and integration with gtars for tokenization. Use cases: region similarity searches, dimension reduction of chromatin accessibility data, scATAC-seq clustering and cell-type annotation, metadata-aware genomic queries, universe construction for standardized references, and any ML task requiring genomic region feature vectors
- **gtars** - High-performance Rust toolkit for genomic interval analysis providing specialized tools for overlap detection using IGD (Integrated Genome Database) indexing, coverage track generation (uniwig module for WIG/BigWig formats), genomic tokenization for machine learning applications (TreeTokenizer for deep learning models), reference sequence management (refget protocol compliance), fragment processing for single-cell genomics (barcode-based splitting and cluster analysis), and fragment scoring against reference datasets. Offers Python bindings with NumPy integration, command-line tools (gtars-cli), and Rust library. Key modules include: tokenizers (convert genomic regions to ML tokens), overlaprs (efficient overlap computation), uniwig (ATAC-seq/ChIP-seq/RNA-seq coverage profiles), refget (GA4GH-compliant sequence digests), bbcache (BEDbase.org integration), scoring (fragment enrichment metrics), and fragsplit (single-cell fragment manipulation). Supports parallel processing, memory-mapped files, streaming for large datasets, and serves as foundation for geniml genomic ML package. Ideal for genomic ML preprocessing, regulatory element analysis, variant annotation, chromatin accessibility profiling, and computational genomics workflows
- **Polars-Bio** - High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Provides overlap, nearest, merge, coverage, complement, and subtract operations for BED/VCF/BAM/GFF intervals. Streaming and cloud-native architecture for large-scale genomic analyses, serving as a faster alternative to bioframe
- **pysam** - Read, write, and manipulate genomic data files (SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences) with pileup analysis, coverage calculations, and bioinformatics workflows
- **PyDESeq2** - Python implementation of the DESeq2 differential gene expression analysis method for bulk RNA-seq data. Provides statistical methods for determining differential expression between experimental conditions using negative binomial generalized linear models. Key features include: size factor estimation for library size normalization, dispersion estimation and shrinkage, hypothesis testing with Wald test or likelihood ratio test, multiple testing correction (Benjamini-Hochberg FDR), results filtering and ranking, and integration with pandas DataFrames. Handles complex experimental designs, batch effects, and replicates. Produces fold-change estimates, p-values, and adjusted p-values for each gene. Use cases: identifying differentially expressed genes between conditions, RNA-seq experiment analysis, biomarker discovery, and gene expression studies requiring rigorous statistical analysis
- **Scanpy** - Comprehensive Python toolkit for single-cell RNA-seq data analysis built on AnnData (scanpy 1.12.x; Python 3.12+). Provides end-to-end workflows for preprocessing (quality control, scrublet doublet detection, normalization, log transformation), dimensionality reduction (PCA, UMAP, t-SNE), Leiden clustering, marker gene identification, pseudobulk aggregation via `get.aggregate()`, trajectory inference (PAGA, diffusion maps), and visualization. Key features include: efficient handling of large datasets using sparse matrices and experimental Dask out-of-core support, integration with scvi-tools for advanced analysis, batch correction methods (ComBat), and publication-quality plotting. Optional GPU acceleration via rapids-singlecell. Use cases: single-cell RNA-seq analysis, cell-type identification, exploratory cluster markers, pseudobulk DE workflows (with pydeseq2), trajectory analysis, and comprehensive single-cell genomics workflows
- **scVelo** - RNA velocity analysis for estimating cell state transitions from unspliced/spliced mRNA dynamics. Infers trajectory directions, computes latent time, and identifies driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference, enabling the study of cellular differentiation dynamics and lineage decisions at single-cell resolution
- **scvi-tools** - Probabilistic deep learning models for single-cell omics analysis. PyTorch-based framework providing variational autoencoders (VAEs) for dimensionality reduction, batch correction, differential expression, and data integration across modalities. Includes 25+ models: scVI/scANVI (RNA-seq integration and cell type annotation), totalVI (CITE-seq protein+RNA), MultiVI (multiome RNA+ATAC integration), PeakVI (ATAC-seq analysis), DestVI/Stereoscope/Tangram (spatial transcriptomics deconvolution), MethylVI (methylation), CytoVI (flow/mass cytometry), VeloVI (RNA velocity), contrastiveVI (perturbation studies), and Solo (doublet detection). Supports seamless integration with Scanpy/AnnData ecosystem, GPU acceleration, reference mapping (scArches), and probabilistic differential expression with uncertainty quantification
- **scikit-bio** - Python library for bioinformatics providing data structures, algorithms, and parsers for biological sequence analysis. Built on NumPy, SciPy, and pandas. Key features include: sequence objects (DNA, RNA, protein sequences) with biological alphabet validation, sequence alignment algorithms (local, global, semiglobal), phylogenetic tree manipulation, diversity metrics (alpha diversity, beta diversity, phylogenetic diversity), distance metrics for sequences and communities, file format parsers (FASTA, FASTQ, QIIME formats, Newick), and statistical analysis tools. Provides scikit-learn compatible transformers for machine learning workflows. Supports efficient processing of large sequence datasets. Use cases: sequence analysis, microbial ecology (16S rRNA analysis), metagenomics, phylogenetic analysis, and bioinformatics research requiring sequence manipulation and diversity calculations
- **TileDB-VCF** - High-performance C++ library with Python and CLI interfaces for efficient storage and retrieval of genomic variant-call data using TileDB multidimensional sparse array technology. Enables scalable VCF/BCF ingestion with incremental sample addition, compressed storage, parallel queries across genomic regions and samples, and export capabilities for population genomics workflows. Key features include: memory-efficient queries, cloud storage integration (S3, Azure, GCS), and CLI tools for dataset creation, sample ingestion, data export, and statistics. Supports building variant databases for large cohorts, population-scale genomics studies, and association analysis. Use cases: population genomics databases, cohort studies, variant discovery workflows, genomic data warehousing, and scaling to enterprise-level analysis with TileDB-Cloud platform
- **Zarr** - Python library (Zarr-Python 3.x) implementing chunked, compressed N-dimensional arrays for local disk and cloud object storage (S3, GCS via fsspec). Supports Zarr format 2 and 3, `zarr.codecs` compression (Blosc, gzip, zstd), partial chunk reads, consolidated metadata, sharding, and integration with NumPy, Dask, and Xarray. Use for out-of-core arrays, cloud-native pipelines, and large scientific datasets (genomics, imaging, climate). Skill: `zarr-python`

### Data Management & Infrastructure
- **LaminDB** - Open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable). Provides unified platform combining lakehouse architecture, lineage tracking, feature stores, biological ontologies (via Bionty plugin with 20+ ontologies: genes, proteins, cell types, tissues, diseases, pathways), LIMS, and ELN capabilities through a single Python API. Key features include: automatic data lineage tracking (code, inputs, outputs, environment), versioned artifacts (DataFrame, AnnData, SpatialData, Parquet, Zarr), schema validation and data curation with standardization/synonym mapping, queryable metadata with feature-based filtering, cross-registry traversal, and streaming for large datasets. Supports integrations with workflow managers (Nextflow, Snakemake, Redun), MLOps platforms (Weights & Biases, MLflow, HuggingFace, scVI-tools), cloud storage (S3, GCS, S3-compatible), array stores (TileDB-SOMA, DuckDB), and visualization (Vitessce). Deployment options: local SQLite, cloud storage with SQLite, or cloud storage with PostgreSQL for production. Use cases: scRNA-seq standardization and analysis, flow cytometry/spatial data management, multi-modal dataset integration, computational workflow tracking with reproducibility, biological ontology-based annotation, data lakehouse construction for unified queries, ML pipeline integration with experiment tracking, and FAIR-compliant dataset publishing
- **Modal** - Serverless cloud platform for running Python code with minimal configuration, specialized for AI/ML workloads and scientific computing. Execute functions on powerful GPUs (T4, L4, A10, A100, L40S, H100, H200, B200, B200+), scale automatically from zero to thousands of containers, and pay only for compute used. Key features include: declarative container image building with uv (recommended)/pip/apt package management, automatic autoscaling with configurable limits and buffer containers, GPU acceleration with multi-GPU support (up to 8 GPUs per container, up to 1,536 GB VRAM), persistent storage via Volumes (v1 and v2) for model weights and datasets, secret management for API keys and credentials, scheduled jobs with cron expressions, web endpoints for deploying serverless APIs (FastAPI, ASGI, WSGI, WebSockets), parallel execution with `.map()` for batch processing, input concurrency and dynamic batching for I/O-bound workloads, and resource configuration (CPU cores, memory, ephemeral disk up to 3 TiB). Supports custom Docker images, Micromamba/Conda environments, integration with Hugging Face/Weights & Biases, and distributed multi-GPU training. Free tier includes $30/month credits. Use cases: ML model deployment and inference (LLMs, image generation, speech, embeddings), GPU-accelerated training and fine-tuning, batch processing large datasets in parallel, scheduled compute-intensive jobs, serverless API deployment with autoscaling, protein folding and computational biology, scientific computing requiring distributed compute or specialized hardware, and data pipeline automation
- **Optimize for GPU** - GPU-accelerate Python code using the NVIDIA RAPIDS ecosystem and related libraries for 10x–1000x speedups on suitable workloads. Covers 12 GPU libraries with decision framework for choosing the right tool: CuPy (drop-in NumPy/SciPy replacement for array operations, FFT, linear algebra), Numba CUDA (custom GPU kernels with fine-grained thread/block/shared-memory control), Warp (JIT-compiled simulation kernels with built-in spatial types for physics, mesh ray casting, differentiable programming, and robotics), cuDF (drop-in pandas replacement for dataframe ETL, groupby, joins), cuML (drop-in scikit-learn replacement for classification, regression, clustering, dimensionality reduction, preprocessing), cuGraph (drop-in NetworkX replacement for PageRank, centrality, community detection, shortest paths), KvikIO (GPUDirect Storage for high-performance file IO bypassing CPU memory, S3/HTTP direct-to-GPU reads, Zarr GPU backend), cuxfilter (GPU-accelerated interactive cross-filtering dashboards with Bokeh, Datashader, and Deck.gl), cuCIM (drop-in scikit-image replacement for image filtering, morphology, segmentation, plus fast whole-slide image reading for digital pathology), cuVS (GPU-accelerated vector/similarity search with CAGRA, IVF-Flat, IVF-PQ for RAG and recommender systems), cuSpatial (GPU-accelerated GeoPandas replacement for spatial joins, point-in-polygon, trajectory analysis), and RAFT/pylibraft (sparse eigensolvers, device memory management, multi-GPU communication). All libraries interoperate via CUDA Array Interface for zero-copy data sharing. Includes optimization workflow (profile first, assess GPU suitability, start with drop-in replacements, minimize host-device transfers), code transformation patterns for each library, memory management principles, and common pitfalls. Use cases: accelerating NumPy/pandas/scikit-learn/NetworkX/scikit-image/GeoPandas/Faiss workloads, physics simulation, differentiable rendering, particle systems, vector search for RAG pipelines, GPUDirect Storage file IO, interactive data exploration dashboards, geospatial analysis, medical imaging, and sparse eigenvalue problems

### Cheminformatics & Drug Discovery
- **Datamol** - Python library for molecular manipulation and featurization built on RDKit with enhanced workflows and performance optimizations. Provides utilities for molecular I/O (reading/writing SMILES, SDF, MOL files), molecular standardization and sanitization, molecular transformations (tautomer enumeration, stereoisomer generation), molecular featurization (descriptors, fingerprints, graph representations), parallel processing for large datasets, and integration with machine learning pipelines. Features include: optimized RDKit operations, caching for repeated computations, molecular filtering and preprocessing, and seamless integration with pandas DataFrames. Designed for drug discovery and cheminformatics workflows requiring efficient processing of large compound libraries. Use cases: molecular preprocessing for ML models, compound library management, molecular similarity searches, and cheminformatics data pipelines
- **DeepChem** - Molecular machine learning library (PyPI 2.8.0; Python 3.7–3.11) with TensorFlow, PyTorch, and JAX backends. Graph neural networks (GCN, GAT, MPNN, AttentiveFP), 30+ MoleculeNet benchmarks, diverse featurizers (fingerprints, descriptors, graphs), and pretrained models (ChemBERTa, GROVER, MolFormer). Install backend-specific extras (`deepchem[torch]`, `[tensorflow]`, `[jax]`). Use for ADMET/toxicity prediction, materials properties, and transfer learning on small datasets
- **DiffDock** - State-of-the-art diffusion-based molecular docking method for predicting protein-ligand binding poses and binding affinities. Uses diffusion models to generate diverse, high-quality binding poses without requiring exhaustive search. Key features include: fast inference compared to traditional docking methods, generation of multiple diverse poses, confidence scoring for predictions, and support for flexible ligand docking. Provides pre-trained models and Python API for integration into drug discovery pipelines. Achieves superior performance on standard benchmarks (PDBbind, CASF) compared to traditional docking methods. Use cases: virtual screening, lead optimization, binding pose prediction, structure-based drug design, and initial pose generation for refinement with more expensive methods
- **MedChem** - Python library for molecular filtering and prioritization in drug discovery (datamol-io). Apply literature-derived drug-likeness rules (Lipinski, Veber, CNS, lead-like), named structural alert catalogs (PAINS, Brenk, NIBR), complexity thresholds against ZINC-derived percentiles, chemical group detection, and a custom query language for multi-criteria filtering. Returns pandas DataFrames from rule/structural filters and boolean masks from the functional API. Integrates with datamol/RDKit and supports parallel processing. Use cases: compound library triage, hit-to-lead filtering, PAINS deprioritization, screening-deck curation, and lead optimization workflows
- **Molfeat** - Comprehensive Python library providing 100+ molecular featurizers for converting molecules into numerical representations suitable for machine learning. Includes molecular fingerprints (ECFP, MACCS, RDKit, Pharmacophore), molecular descriptors (2D/3D descriptors, constitutional, topological, electronic), graph-based representations (molecular graphs, line graphs), and pre-trained models (MolBERT, ChemBERTa, Uni-Mol embeddings). Features unified API across different featurizer types, caching for performance, parallel processing, and integration with popular ML frameworks (scikit-learn, PyTorch, TensorFlow). Supports both traditional cheminformatics descriptors and modern learned representations. Use cases: molecular property prediction, virtual screening, molecular similarity searches, and preparing molecular data for machine learning models
- **PyTDC** - Python library providing access to Therapeutics Data Commons (TDC), a collection of curated datasets and benchmarks for drug discovery and development. Includes datasets for ADMET prediction (absorption, distribution, metabolism, excretion, toxicity), drug-target interactions, drug-drug interactions, drug response prediction, molecular generation, and retrosynthesis. Features standardized data formats, data loaders with automatic preprocessing, benchmark tasks with evaluation metrics, leaderboards for model comparison, and integration with popular ML frameworks. Provides both single-molecule and drug-pair datasets, covering various stages of drug discovery from target identification to clinical outcomes. Use cases: benchmarking ML models for drug discovery, ADMET prediction model development, drug-target interaction prediction, and drug discovery research
- **RDKit** - Open-source cheminformatics toolkit for molecular informatics and drug discovery. Provides comprehensive functionality for molecular I/O (reading/writing SMILES, SDF, MOL, PDB files), molecular descriptors (200+ 2D and 3D descriptors), molecular fingerprints (Morgan, RDKit, MACCS, topological torsions), SMARTS pattern matching for substructure searches, molecular alignment and 3D coordinate generation, pharmacophore perception, reaction handling, and molecular drawing. Features high-performance C++ core with Python bindings, support for large molecule sets, and extensive documentation. Widely used in pharmaceutical industry and academic research. Use cases: molecular property calculation, virtual screening, molecular similarity searches, substructure matching, molecular visualization, and general cheminformatics workflows
- **Rowan** - Cloud-based quantum chemistry platform with Python API for computational chemistry workflows. Provides access to 45+ chemistry calculations including pKa prediction, redox potentials, solubility, conformer searching, geometry optimization, protein-ligand docking (AutoDock Vina), and AI-powered protein cofolding (Chai-1, Boltz-1/2). Supports DFT, semiempirical (GFN-xTB), and neural network potential methods (AIMNet2, Egret). Key features include: automatic cloud resource allocation, unified API for diverse computational methods, RDKit-native interface for seamless cheminformatics integration, workflow organization with folders and projects, batch processing, and web interface for visualization. Requires API key from labs.rowansci.com. Use cases: molecular property prediction, structure-based drug design, virtual screening campaigns, protein-ligand binding prediction, conformational analysis, and automated computational chemistry pipelines
- **TorchDrug** - PyTorch-based machine learning platform for drug discovery with 40+ datasets, 20+ GNN models for molecular property prediction, protein modeling, knowledge graph reasoning, molecular generation, and retrosynthesis planning

### Proteomics & Mass Spectrometry
- **matchms** - Processing and similarity matching of mass spectrometry data with 40+ filters, spectral library matching (Cosine, Modified Cosine, Neutral Losses), metadata harmonization, molecular fingerprint comparison, and support for multiple file formats (MGF, MSP, mzML, JSON)
- **pyOpenMS** - Comprehensive mass spectrometry data analysis for proteomics and metabolomics (LC-MS/MS processing, peptide identification, feature detection, quantification, chemical calculations, and integration with search engines like Comet, Mascot, MSGF+)

### Medical Imaging & Digital Pathology
- **histolab** - Digital pathology toolkit for whole slide image (WSI) processing and analysis. Provides automated tissue detection, tile extraction for deep learning pipelines, and preprocessing for gigapixel histopathology images. Key features include: multi-format WSI support (SVS, TIFF, NDPI), three tile extraction strategies (RandomTiler for sampling, GridTiler for complete coverage, ScoreTiler for quality-driven selection), automated tissue masks with customizable filters, built-in scorers (NucleiScorer, CellularityScorer), Macenko and Reinhard stain normalization (0.6.0+), pyramidal image handling, visualization tools (thumbnails, mask overlays, tile previews), and H&E stain decomposition. Supports multiple tissue sections, artifact removal, pen annotation exclusion, and reproducible extraction with seeding. Requires Python 3.8–3.11, OpenSlide, and Linux or macOS. Use cases: creating training datasets for computational pathology, extracting informative tiles for tumor classification, whole-slide tissue characterization, quality assessment of histology samples, automated nuclei density analysis, and preprocessing for digital pathology deep learning workflows
- **PathML** - Comprehensive computational pathology toolkit for whole slide image analysis, tissue segmentation, and machine learning on pathology data. Provides end-to-end workflows for digital pathology research including data loading, preprocessing, feature extraction, and model deployment
- **pydicom** - Pure Python package for working with DICOM (Digital Imaging and Communications in Medicine) files. Provides comprehensive support for reading, writing, and manipulating medical imaging data from CT, MRI, X-ray, ultrasound, PET scans and other modalities. Key features include: pixel data extraction and manipulation with automatic decompression (JPEG/JPEG 2000/RLE), metadata access and modification with 1000+ standardized DICOM tags, image format conversion (PNG/JPEG/TIFF), anonymization tools for removing Protected Health Information (PHI), windowing and display transformations (VOI LUT application), multi-frame and 3D volume processing, DICOM sequence handling, and support for multiple transfer syntaxes. Use cases: medical image analysis, PACS system integration, radiology workflows, research data processing, DICOM anonymization, format conversion, image preprocessing for machine learning, multi-slice volume reconstruction, and clinical imaging pipelines

### Healthcare AI & Clinical Machine Learning
- **NeuroKit2** - Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Key features include: automated signal processing pipelines (cleaning, peak detection, delineation, quality assessment), heart rate variability analysis across time/frequency/nonlinear domains (SDNN, RMSSD, LF/HF, DFA, entropy measures), EEG analysis (frequency band power, microstates, source localization), autonomic nervous system assessment (sympathetic indices, respiratory sinus arrhythmia), comprehensive complexity measures (25+ entropy types, 15+ fractal dimensions, Lyapunov exponents), event-related and interval-related analysis modes, epoch creation and averaging for stimulus-locked responses, multi-signal integration with unified workflows, and extensive signal processing utilities (filtering, decomposition, peak correction, spectral analysis). Includes modular reference documentation across 12 specialized domains. Use cases: heart rate variability for cardiovascular health assessment, EEG microstates for consciousness studies, electrodermal activity for emotion research, respiratory variability analysis, psychophysiology experiments, affective computing, stress monitoring, sleep staging, autonomic dysfunction assessment, biofeedback applications, and multi-modal physiological signal integration for comprehensive human state monitoring
- **PyHealth** - Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. Provides specialized tools for electronic health records (EHR), physiological signals, medical imaging, and clinical text analysis. Key features include: 10+ healthcare datasets (MIMIC-III/IV, eICU, OMOP, sleep EEG, COVID-19 CXR), 20+ predefined clinical prediction tasks (mortality, hospital readmission, length of stay, drug recommendation, sleep staging, EEG analysis), 33+ models (Logistic Regression, MLP, CNN, RNN, Transformer, GNN, plus healthcare-specific models like RETAIN, SafeDrug, GAMENet, StageNet), comprehensive data processing (sequence processors, signal processors, medical code translation between ICD-9/10, NDC, RxNorm, ATC systems), training/evaluation utilities (Trainer class, fairness metrics, calibration, uncertainty quantification), and interpretability tools (attention visualization, SHAP, ChEFER). 3x faster than pandas for healthcare data processing. Use cases: ICU mortality prediction, hospital readmission risk assessment, safe medication recommendation with drug-drug interaction constraints, sleep disorder diagnosis from EEG signals, medical code standardization and translation, clinical text to ICD coding, length of stay estimation, and any clinical ML application requiring interpretability, fairness assessment, and calibrated predictions for healthcare deployment

### Clinical Documentation & Decision Support
- **Clinical Decision Support** - Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings. Includes patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Features GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration (genomic alterations, gene expression signatures, IHC markers), and regulatory compliance. Use cases: pharmaceutical cohort reporting, clinical guideline development, comparative effectiveness analyses, treatment algorithm creation, and evidence synthesis for drug development
- **Clinical Reports** - Write comprehensive clinical reports following established guidelines and standards. Covers case reports (CARE guidelines), diagnostic reports (radiology, pathology, laboratory), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries). Includes templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use cases: journal case reports, diagnostic findings documentation, clinical trial reporting, patient progress notes, and regulatory submissions
- **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. Features SMART goal frameworks, evidence-based interventions, HIPAA compliance, and professional formatting. Use cases: individualized patient care plans, rehabilitation programs, psychiatric treatment plans, surgical care pathways, and pain management protocols

### Neuroscience & Electrophysiology
- **BIDS** - Brain Imaging Data Structure (BIDS) standard for organizing and describing neuroscience and biomedical research datasets. While originating for MRI, BIDS now covers 11 modalities: imaging (MRI structural/functional/diffusion/perfusion, PET, microscopy), electrophysiology (EEG, MEG, iEEG, EMG), and other data (NIRS, motion capture, behavioral, MR spectroscopy), with active BEPs extending to microelectrode electrophysiology (Neuropixels), stimuli, and more. Covers the BIDS directory hierarchy, file naming conventions with entities (subject, session, task, acquisition, run, etc.), and JSON sidecar metadata. Key features include: dataset creation and validation workflows, querying BIDS datasets with PyBIDS (BIDSLayout), DICOM-to-BIDS conversion using HeuDiConv (ReproIn turnkey, map-into-reproin, and custom heuristic modes), dcm2bids (config-file-based), and BIDScoin (GUI-based), metadata inheritance and sidecar management, events files for task fMRI, participants and scans TSV files, BIDS derivatives conventions for preprocessed data and analysis outputs, BIDS-Apps interface (fMRIPrep, MRIQC, QSIPrep), machine-readable BIDS schema (bids_schema.json) and BEP listing (beps.yml) with update script, and .bidsignore configuration. Includes detailed reference documentation for the complete BIDS specification entity table (35 entities in schema ordering), required and recommended metadata fields for every modality, standard template spaces, and conversion tool workflows with examples. Use cases: organizing neuroscience data for sharing and analysis, validating BIDS compliance before repository submission (OpenNeuro, DANDI), converting DICOM scanner data to BIDS format, creating BIDS-compliant derivatives, querying datasets programmatically, and preparing data for BIDS-Apps processing pipelines
- **Neuropixels-Analysis** - Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using SpikeInterface, Allen Institute, and International Brain Laboratory (IBL) best practices. Supports the full workflow from raw data to publication-ready curated units. Key features include: data loading from SpikeGLX, Open Ephys, and NWB formats, preprocessing pipelines (highpass filtering, phase shift correction for Neuropixels 1.0, bad channel detection, common average referencing), motion/drift estimation and correction (kilosort_like and nonrigid_accurate presets), spike sorting integration (Kilosort4 GPU, SpykingCircus2, Mountainsort5 CPU), comprehensive postprocessing (waveform extraction, template computation, spike amplitudes, correlograms, unit locations), quality metrics computation (SNR, ISI violations, presence ratio, amplitude cutoff, drift metrics), automated curation using Allen Institute and IBL criteria with configurable thresholds, AI-assisted visual curation for uncertain units using Claude API, and export to Phy for manual review or NWB for sharing. Supports Neuropixels 1.0 (960 electrodes, 384 channels) and Neuropixels 2.0 (single and 4-shank configurations). Use cases: extracellular electrophysiology analysis, spike sorting from silicon probes, neural population recordings, systems neuroscience research, unit quality assessment, publication-ready neural data processing, and integration of AI-assisted curation for borderline units

### Protein Engineering & Design
- **Adaptyv** - Cloud laboratory platform for automated protein testing and validation. Submit protein sequences via API or web interface and receive experimental results in approximately 21 days. Supports multiple assay types including binding assays (biolayer interferometry for protein-target interactions, KD/kon/koff measurements), expression testing (quantify protein expression levels in E. coli, mammalian, yeast, or insect cells), thermostability measurements (DSF and CD for Tm determination and thermal stability profiling), and enzyme activity assays (kinetic parameters, substrate specificity, inhibitor testing). Includes computational optimization tools for pre-screening sequences: NetSolP/SoluProt for solubility prediction, SolubleMPNN for sequence redesign to improve expression, ESM for sequence likelihood scoring, ipTM (AlphaFold-Multimer) for interface stability assessment, and pSAE for aggregation risk quantification. Platform features automated workflows from expression through purification to assay execution with quality control, webhook notifications for experiment completion, batch submission support for high-throughput screening, and comprehensive results with kinetic parameters, confidence metrics, and raw data access. Use cases: antibody affinity maturation, therapeutic protein developability assessment, enzyme engineering and optimization, protein stability improvement, AI-driven protein design validation, library screening for expression and function, lead optimization with experimental feedback, and integration of computational design with wet-lab validation in iterative design-build-test-learn cycles
- **ESM (Evolutionary Scale Modeling)** - State-of-the-art protein language models from EvolutionaryScale for protein design, structure prediction, and representation learning. Includes ESM3 (1.4B-98B parameter multimodal generative models for simultaneous reasoning across sequence, structure, and function with chain-of-thought generation, inverse folding, and function-conditioned design) and ESM C (300M-6B parameter efficient embedding models 3x faster than ESM2 for similarity analysis, classification, and feature extraction). Supports local inference with open weights, Forge API (`ESM_API_KEY`) for scalable ESM3/ESM C inference, and Biohub-hosted ESMFold2 for all-atom structure prediction. Use cases: novel protein design, structure prediction from sequence, sequence design from structure, protein embeddings, function annotation, variant generation, and directed evolution workflows
- **Glycoengineering** - Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use for glycoprotein engineering, therapeutic antibody optimization, and vaccine design
- **Molecular Dynamics** - Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). Use for structural biology, drug binding studies, and biophysics research

### Machine Learning & Deep Learning
- **aeon** - Comprehensive scikit-learn compatible Python toolkit for time series machine learning providing state-of-the-art algorithms across 7 domains: classification (13 algorithm categories including ROCKET variants, deep learning with InceptionTime/ResNet/FCN, distance-based with DTW/ERP/LCSS, shapelet-based, dictionary methods like BOSS/WEASEL, and hybrid ensembles HIVECOTE), regression (9 categories mirroring classification approaches), clustering (k-means/k-medoids with temporal distances, deep learning autoencoders, spectral methods), forecasting (ARIMA, ETS, Theta, Threshold Autoregressive, TCN, DeepAR), anomaly detection (STOMP/MERLIN matrix profile, clustering-based CBLOF/KMeans, isolation methods, copula-based COPOD), segmentation (ClaSP, FLUSS, HMM, binary segmentation), and similarity search (MASS algorithm, STOMP motif discovery, approximate nearest neighbors). Includes 40+ distance metrics (elastic: DTW/DDTW/WDTW/Shape-DTW, edit-based: ERP/EDR/LCSS/TWE/MSM, lock-step: Euclidean/Manhattan), extensive transformations (ROCKET/MiniRocket/MultiRocket for features, Catch22/TSFresh for statistics, SAX/PAA for symbolic representation, shapelet transforms, wavelets, matrix profile), 20+ deep learning architectures (FCN, ResNet, InceptionTime, TCN, autoencoders with attention mechanisms), comprehensive benchmarking tools (UCR/UEA archives with 100+ datasets, published results repository, statistical testing), and performance-optimized implementations using numba. Features progressive model complexity from fast baselines (MiniRocket: <1 second training, 0.95+ accuracy on many benchmarks) to state-of-the-art ensembles (HIVECOTE V2), GPU acceleration support, and extensive visualization utilities. Use cases: physiological signal classification (ECG, EEG), industrial sensor monitoring, financial forecasting, change point detection, pattern discovery, activity recognition from wearables, predictive maintenance, climate time series analysis, and any sequential data requiring specialized temporal modeling beyond standard ML
- **Cirq** - Google quantum computing framework for designing, simulating, and running quantum circuits. Best suited for targeting Google Quantum AI hardware, designing noise-aware circuits, and running quantum characterization experiments. Provides low-level circuit design, noise modeling, and hardware-specific optimizations. For IBM hardware use Qiskit; for quantum ML with autodiff use PennyLane; for physics simulations use QuTiP
- **PufferLib** - High-performance reinforcement learning library achieving 1M-4M steps/second through optimized vectorization, native multi-agent support, and efficient PPO training (PuffeRL). Use this skill for RL training on any environment (Gymnasium, PettingZoo, Atari, Procgen), creating custom PufferEnv environments, developing policies (CNN, LSTM, multi-input architectures), optimizing parallel simulation performance, or scaling multi-agent systems. Includes Ocean suite (20+ environments), seamless framework integration with automatic space flattening, zero-copy vectorization with shared memory buffers, distributed training support, and comprehensive reference guides for training workflows, environment development, vectorization optimization, policy architectures, and third-party integrations
- **PyMC** - Comprehensive Python library for Bayesian statistical modeling and probabilistic programming. Provides intuitive syntax for building probabilistic models, advanced MCMC sampling algorithms (NUTS, Metropolis-Hastings, Slice sampling), variational inference methods (ADVI, SVGD), Gaussian processes, time series models (ARIMA, state space models), and model comparison tools (WAIC, LOO). Features include: automatic differentiation via Aesara (formerly Theano), GPU acceleration support, parallel sampling, model diagnostics and convergence checking, and integration with ArviZ for visualization and analysis. Supports hierarchical models, mixture models, survival analysis, and custom distributions. Use cases: Bayesian data analysis, uncertainty quantification, A/B testing, time series forecasting, hierarchical modeling, and probabilistic machine learning
- **PyMOO** - Python framework for multi-objective optimization using evolutionary algorithms. Provides implementations of state-of-the-art algorithms including NSGA-II, NSGA-III, MOEA/D, SPEA2, and reference-point based methods. Features include: support for constrained and unconstrained optimization, multiple problem types (continuous, discrete, mixed-variable), performance indicators (hypervolume, IGD, GD), visualization tools (Pareto front plots, convergence plots), and parallel evaluation support. Supports custom problem definitions, algorithm configuration, and result analysis. Designed for engineering design, parameter optimization, and any problem requiring optimization of multiple conflicting objectives simultaneously. Use cases: multi-objective optimization problems, Pareto-optimal solution finding, engineering design optimization, and research in evolutionary computation
- **PyTorch Lightning** - Deep learning framework (lightning 2.6+) that organizes PyTorch code to eliminate boilerplate while maintaining full flexibility. Automates training workflows (epoch/batch iteration, optimizer steps, gradient management, checkpointing), supports multi-GPU/TPU training with DDP/FSDP/DeepSpeed strategies, includes LightningModule for model organization, Trainer for automation, LightningDataModule for data pipelines, callbacks for extensibility, and integrations with TensorBoard, Wandb, and MLflow for experiment tracking
- **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/NumPy, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ). Key features include: quantum circuit construction with QNodes (quantum functions with automatic differentiation), 100+ quantum gates and operations (Pauli, Hadamard, rotation, controlled gates), circuit templates and layers for common ansatze (StronglyEntanglingLayers, BasicEntanglerLayers, UCCSD for chemistry), gradient computation methods (parameter-shift rule for hardware, backpropagation for simulators, adjoint differentiation), quantum chemistry module (molecular Hamiltonian construction, VQE for ground state energy, differentiable Hartree-Fock solver), ML framework integration (TorchLayer for PyTorch models, JAX transformations, TensorFlow deprecated), built-in optimizers (Adam, GradientDescent, QNG, Rotosolve), measurement types (expectation values, probabilities, samples, state vectors), device ecosystem (default.qubit simulator, lightning.qubit for performance, hardware plugins for IBM/Braket/Cirq/Rigetti/IonQ), and Catalyst for just-in-time compilation with adaptive circuits. Supports variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, data encoding strategies (angle, amplitude, IQP embeddings), and pulse-level programming. Use cases: variational quantum eigensolver for molecular simulations, quantum circuit machine learning with gradient-based optimization, hybrid quantum-classical neural networks, quantum chemistry calculations with differentiable workflows, quantum algorithm prototyping with hardware-agnostic code, quantum machine learning research with automatic differentiation, and deploying quantum circuits across multiple quantum computing platforms
- **Qiskit** - World's most popular open-source quantum computing framework for building, optimizing, and executing quantum circuits with 13M+ downloads and 74% developer preference. Provides comprehensive tools for quantum algorithm development including circuit construction with 100+ quantum gates (Pauli, Hadamard, CNOT, rotation gates, controlled gates), circuit transpilation with 83x faster optimization than competitors producing circuits with 29% fewer two-qubit gates, primitives for execution (Sampler for bitstring measurements and probability distributions, Estimator for expectation values and observables), visualization tools (circuit diagrams in matplotlib/LaTeX, result histograms, Bloch sphere, state visualizations), backend-agnostic execution (local simulators including StatevectorSampler and Aer, IBM Quantum hardware with 100+ qubit systems, IonQ trapped ion, Amazon Braket multi-provider), session and batch modes for iterative and parallel workloads, error mitigation with configurable resilience levels (readout error correction, ZNE, PEC reducing sampling overhead by 100x), four-step patterns workflow (Map classical problems to quantum circuits, Optimize through transpilation, Execute with primitives, Post-process results), algorithm libraries including Qiskit Nature for quantum chemistry (molecular Hamiltonians, VQE for ground states, UCCSD ansatz, multiple fermion-to-qubit mappings), Qiskit Optimization for combinatorial problems (QAOA, portfolio optimization, MaxCut), and Qiskit Machine Learning (quantum kernels, VQC, QNN), support for Python/C/Rust with modular architecture, parameterized circuits for variational algorithms, quantum Fourier transform, Grover search, Shor's algorithm, pulse-level control, IBM Quantum Runtime for cloud execution with job management and queuing, and comprehensive documentation with textbook and tutorials. Use cases: variational quantum eigensolver for molecular ground state energy, QAOA for combinatorial optimization problems, quantum chemistry simulations with multiple ansatze and mappings, quantum machine learning with kernel methods and neural networks, hybrid quantum-classical algorithms, quantum algorithm research and prototyping across multiple hardware platforms, quantum circuit optimization and benchmarking, quantum error mitigation and characterization, quantum information science experiments, and production quantum computing workflows on real quantum hardware
- **QuTiP** - Quantum Toolbox in Python for simulating and analyzing quantum mechanical systems. Provides comprehensive tools for both closed (unitary) and open (dissipative) quantum systems including quantum states (kets, bras, density matrices, Fock states, coherent states), quantum operators (creation/annihilation operators, Pauli matrices, angular momentum operators, quantum gates), time evolution solvers (Schrödinger equation with sesolve, Lindblad master equation with mesolve, quantum trajectories with Monte Carlo mcsolve, Bloch-Redfield brmesolve, Floquet methods for periodic Hamiltonians), analysis tools (expectation values, entropy measures, fidelity, concurrence, correlation functions, steady state calculations), visualization (Bloch sphere with animations, Wigner functions, Q-functions, Fock distributions, matrix histograms), and advanced methods (Hierarchical Equations of Motion for non-Markovian dynamics, permutational invariance for identical particles, stochastic solvers, superoperators). Supports tensor products for composite systems, partial traces, time-dependent Hamiltonians, multiple dissipation channels, and parallel processing. Includes extensive documentation, tutorials, and examples. Use cases: quantum optics simulations (cavity QED, photon statistics), quantum computing (gate operations, circuit dynamics), open quantum systems (decoherence, dissipation), quantum information theory (entanglement dynamics, quantum channels), condensed matter physics (spin chains, many-body systems), and general quantum mechanics research and education
- **scikit-learn** - Industry-standard Python library for classical machine learning (current stable **1.8.0**, Python 3.11–3.14, free-threaded CPython wheels). Provides comprehensive supervised learning (classification: Logistic Regression, SVM, Decision Trees, Random Forests with 17+ variants, Gradient Boosting with XGBoost-compatible HistGradientBoosting, Naive Bayes, KNN, Neural Networks/MLP; regression: Linear, Ridge, Lasso, ElasticNet, SVR, ensemble methods), unsupervised learning (clustering: K-Means, DBSCAN, native HDBSCAN since 1.3, OPTICS, Agglomerative/Hierarchical, Spectral, Gaussian Mixture Models, BIRCH, MeanShift; dimensionality reduction: PCA, Kernel PCA, t-SNE, Isomap, LLE, MDS, ClassicalMDS, NMF, TruncatedSVD, FastICA, LDA; outlier detection: IsolationForest, LocalOutlierFactor, OneClassSVM), data preprocessing (scaling: StandardScaler, MinMaxScaler, RobustScaler; encoding: OneHotEncoder, OrdinalEncoder, LabelEncoder; imputation: SimpleImputer, KNNImputer, IterativeImputer; feature engineering: PolynomialFeatures, KBinsDiscretizer, text vectorization with CountVectorizer/TfidfVectorizer), model evaluation (cross-validation: KFold, StratifiedKFold, TimeSeriesSplit, GroupKFold; hyperparameter tuning: GridSearchCV, RandomizedSearchCV, HalvingGridSearchCV; metrics: 30+ evaluation metrics for classification/regression/clustering including accuracy, precision, recall, F1, ROC-AUC, MSE, RMSE via root_mean_squared_error, R², silhouette score), and Pipeline/ColumnTransformer for production-ready workflows. Features consistent API (fit/predict/transform), extensive documentation, integration with NumPy/pandas/SciPy, joblib persistence, and scikit-learn-compatible ecosystem (XGBoost, LightGBM, CatBoost, imbalanced-learn, UMAP via umap-learn). Optimized implementations using Cython/OpenMP for performance. Use cases: predictive modeling, customer segmentation, anomaly detection, feature engineering, model selection/validation, text classification, image classification (with feature extraction), time series forecasting (with preprocessing), medical diagnosis, fraud detection, recommendation systems, and any tabular data ML task requiring interpretable models or established algorithms
- **scikit-survival** - Survival analysis and time-to-event modeling with censored data. Built on scikit-learn, provides Cox proportional hazards models (CoxPHSurvivalAnalysis, CoxnetSurvivalAnalysis with elastic net regularization), ensemble methods (Random Survival Forests, Gradient Boosting), Survival Support Vector Machines (linear and kernel), non-parametric estimators (Kaplan-Meier, Nelson-Aalen), competing risks analysis, and specialized evaluation metrics (concordance index, time-dependent AUC, Brier score). Handles right-censored data, integrates with scikit-learn pipelines, and supports feature selection and hyperparameter tuning via cross-validation
- **SHAP** - Model interpretability and explainability using Shapley values from game theory. Provides unified approach to explain any ML model with TreeExplainer (fast exact explanations for XGBoost/LightGBM/Random Forest), DeepExplainer (TensorFlow/PyTorch neural networks), KernelExplainer (model-agnostic), and LinearExplainer. Includes comprehensive visualizations (waterfall plots for individual predictions, beeswarm plots for global importance, scatter plots for feature relationships, bar/force/heatmap plots), supports model debugging, fairness analysis, feature engineering guidance, and production deployment
- **Stable Baselines3** - PyTorch-based reinforcement learning library (current stable **2.8.0**, Python 3.10+, PyTorch >= 2.3). Provides reliable implementations of RL algorithms (PPO, SAC, DQN, TD3, DDPG, A2C, HER, RecurrentPPO via SB3-Contrib). Use this skill for training RL agents on standard or custom Gymnasium environments, implementing callbacks for monitoring and control, using vectorized environments for parallel training, creating custom environments with proper Gymnasium API implementation, and integrating with deep RL workflows. Includes comprehensive training templates, evaluation utilities, algorithm selection guidance (on-policy vs off-policy, continuous vs discrete actions), support for multi-input policies (dict observations), goal-conditioned learning with HER, and integration with TensorBoard for experiment tracking
- **statsmodels** - Statistical modeling and econometrics (OLS, GLM, logit/probit, ARIMA, time series forecasting, hypothesis testing, diagnostics)
- **TimesFM Forecasting** - Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use
- **Torch Geometric** - PyTorch Geometric (PyG 2.7.x) for graph neural networks on PyTorch 2.6+. Covers `Data`/`HeteroData`, 60+ conv layers (GCN, GAT, GraphSAGE, GIN), node/link/graph classification, heterogeneous graphs, neighbor sampling (`NeighborLoader`, `LinkNeighborLoader`), OGB and built-in datasets, custom dataset loading, GNN explainability, and scaling via DDP, Lightning, and `torch.compile`
- **Transformers** - Hugging Face Transformers 5.x (PyTorch) for NLP, computer vision, audio, and multimodal tasks. Provides 1M+ pre-trained Hub models via pipelines (text-classification, NER, QA, summarization, translation, text-generation, image-classification, object-detection, ASR, VQA), Trainer API fine-tuning with mixed precision and distributed training, flexible text generation (greedy, beam search, sampling), and Auto classes for architecture selection (BERT, GPT, T5, ViT, BART, etc.)
- **UMAP-learn** - Python implementation of Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and manifold learning. Provides fast, scalable nonlinear dimensionality reduction that preserves both local and global structure of high-dimensional data. Key features include: support for both supervised and unsupervised dimensionality reduction, ability to handle mixed data types, integration with scikit-learn API, and efficient implementation using numba for performance. Produces low-dimensional embeddings (typically 2D or 3D) suitable for visualization and downstream analysis. Often outperforms t-SNE in preserving global structure while maintaining local neighborhoods. Use cases: data visualization, feature extraction, preprocessing for machine learning, single-cell data analysis, and exploratory data analysis of high-dimensional datasets

### Materials Science & Chemistry
- **Astropy** - Comprehensive Python library for astronomy and astrophysics providing core functionality for astronomical research and data analysis. Includes coordinate system transformations (ICRS, Galactic, FK5, AltAz), physical units and quantities with automatic dimensional consistency, FITS file operations (reading, writing, manipulating headers and data), cosmological calculations (luminosity distance, lookback time, Hubble parameter, Planck/WMAP models), precise time handling across multiple time scales (UTC, TAI, TT, TDB) and formats (JD, MJD, ISO), table operations with unit support (FITS, CSV, HDF5, VOTable), WCS transformations between pixel and world coordinates, astronomical constants, modeling framework, visualization tools, and statistical functions. Use for celestial coordinate transformations, unit conversions, FITS image/table processing, cosmological distance calculations, barycentric time corrections, catalog cross-matching, and astronomical data analysis
- **COBRApy** - Python package for constraint-based reconstruction and analysis (COBRA) of metabolic networks. Provides tools for building, manipulating, and analyzing genome-scale metabolic models (GEMs). Key features include: flux balance analysis (FBA) for predicting optimal metabolic fluxes, flux variability analysis (FVA), gene knockout simulations, pathway analysis, model validation, and integration with other COBRA Toolbox formats (SBML, JSON). Supports various optimization objectives (biomass production, ATP production, metabolite production), constraint handling (reaction bounds, gene-protein-reaction associations), and model comparison. Includes utilities for model construction, gap filling, and model refinement. Use cases: metabolic engineering, systems biology, biotechnology applications, understanding cellular metabolism, and predicting metabolic phenotypes
- **Pymatgen** - Python Materials Genomics (pymatgen) library for materials science computation and analysis. Provides comprehensive tools for crystal structure manipulation, phase diagram construction, electronic structure analysis, and materials property calculations. Key features include: structure objects with symmetry analysis, space group determination, structure matching and comparison, phase diagram generation from formation energies, band structure and density of states analysis, defect calculations, surface and interface analysis, and integration with DFT codes (VASP, Quantum ESPRESSO, ABINIT). Supports Materials Project database integration, structure file I/O (CIF, POSCAR, VASP), and high-throughput materials screening workflows. Use cases: materials discovery, crystal structure analysis, phase stability prediction, electronic structure calculations, and computational materials science research

### Engineering & Simulation
- **MATLAB/Octave** - Numerical computing environment for matrix operations, data analysis, visualization, and scientific computing. MATLAB is commercial software optimized for matrix operations, while GNU Octave is a free open-source alternative with high compatibility. Key features include: matrix operations (creation, manipulation, linear algebra), comprehensive mathematics (eigenvalues, SVD, FFT, ODEs, optimization, statistics), 2D/3D visualization (plot, surf, contour, with extensive customization), data import/export (CSV, Excel, MAT files, images), programming constructs (functions, scripts, control flow, OOP), signal processing (FFT, filtering, convolution), and Python integration (calling Python from MATLAB and vice versa). Supports vectorized operations for performance, anonymous functions, tables for mixed data types, and cell arrays for heterogeneous data. GNU Octave provides compatibility with most MATLAB scripts with minor differences (comments with #, block terminators like endif, compound operators like +=). Scripts can be executed via `matlab -nodisplay -r "run('script.m'); exit;"` or `octave script.m`. Use cases: numerical simulations, signal processing, image processing, control systems, statistical analysis, algorithm prototyping, data visualization, and any scientific computing task requiring matrix operations or numerical methods
- **FluidSim** - Object-oriented Python framework for high-performance computational fluid dynamics (CFD) simulations using pseudospectral methods with FFT. Provides solvers for periodic-domain equations including 2D/3D incompressible Navier-Stokes equations (with/without stratification), shallow water equations, and Föppl-von Kármán elastic plate equations. Key features include: Pythran/Transonic compilation for performance comparable to Fortran/C++, MPI parallelization for large-scale simulations, hierarchical parameter configuration with type safety, comprehensive output management (physical fields in HDF5, spatial means, energy/enstrophy spectra, spectral energy budgets), custom forcing mechanisms (time-correlated random forcing, proportional forcing, script-defined forcing), flexible initial conditions (noise, vortex, dipole, Taylor-Green, from file, in-script), online and offline visualization, and integration with ParaView/VisIt for 3D visualization. Supports workflow features including simulation restart/continuation, parametric studies with batch execution, cluster submission integration, and adaptive CFL-based time stepping. Use cases: 2D/3D turbulence studies with energy cascade analysis, stratified oceanic and atmospheric flows with buoyancy effects, geophysical flows with rotation (Coriolis effects), vortex dynamics and fundamental fluid mechanics research, high-resolution direct numerical simulation (DNS), parametric studies exploring parameter spaces, validation studies (Taylor-Green vortex), and any periodic-domain fluid dynamics research requiring HPC-grade performance with Python flexibility
- **SimPy** - Process-based discrete-event simulation framework for modeling systems with processes, queues, and resource contention (manufacturing, service operations, network traffic, logistics). Supports generator-based process definition, multiple resource types (Resource, PriorityResource, PreemptiveResource, Container, Store), event-driven scheduling, process interaction mechanisms (signaling, interruption, parallel/sequential execution), real-time simulation synchronized with wall-clock time, and comprehensive monitoring capabilities for utilization, wait times, and queue statistics
- **SymPy** - Symbolic mathematics in Python for exact computation using mathematical symbols rather than numerical approximations. Provides comprehensive support for symbolic algebra (simplification, expansion, factorization), calculus (derivatives, integrals, limits, series), equation solving (algebraic, differential, systems of equations), matrices and linear algebra (eigenvalues, decompositions, solving linear systems), physics (classical mechanics with Lagrangian/Hamiltonian formulations, quantum mechanics, vector analysis, units), number theory (primes, factorization, modular arithmetic, Diophantine equations), geometry (2D/3D analytic geometry), combinatorics (permutations, combinations, partitions, group theory), logic and sets, statistics (probability distributions, random variables), special functions (gamma, Bessel, orthogonal polynomials), and code generation (lambdify to NumPy/SciPy functions, C/Fortran code generation, LaTeX output for documentation). Emphasizes exact arithmetic using rational numbers and symbolic representations, supports assumptions for improved simplification (positive, real, integer), integrates seamlessly with NumPy/SciPy through lambdify for fast numerical evaluation, and enables symbolic-to-numeric pipelines for scientific computing workflows

### Data Analysis & Visualization
- **Dask** - Parallel and distributed computing for larger-than-RAM pandas/NumPy workflows (dask 2026.x; Python 3.10+). Provides lazy DataFrames (expression-based query planning since 2025.1), Arrays, Bags, delayed tasks, and Futures via dask.distributed. Scales from multi-core laptops to clusters with a diagnostic dashboard. PyArrow 16+ required for DataFrame I/O; cloud paths need s3fs/gcsfs. Use for parallel file processing, out-of-core ETL, and scaling existing pandas/NumPy code. For single-machine out-of-core analytics without a cluster, consider vaex; for in-memory speed use polars
- **GeoMaster** - Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task
- **GeoPandas** - Python library extending pandas for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Provides GeoDataFrame and GeoSeries data structures combining geometric data with tabular attributes for spatial analysis. Key features include: reading/writing spatial file formats (Shapefile, GeoJSON, GeoPackage, PostGIS, Parquet) with Arrow acceleration for 2-4x faster I/O, geometric operations (buffer, simplify, centroid, convex hull, affine transformations) through Shapely integration, spatial analysis (spatial joins with predicates like intersects/contains/within, nearest neighbor joins, overlay operations for union/intersection/difference, dissolve for aggregation, clipping), coordinate reference system (CRS) management (setting CRS, reprojecting between coordinate systems, UTM estimation), and visualization (static choropleth maps with matplotlib, interactive maps with folium, multi-layer mapping, classification schemes with mapclassify). Supports spatial indexing for performance, filtering during read operations (bbox, mask, SQL WHERE), and integration with cartopy for cartographic projections. Use cases: spatial data manipulation, buffer analysis, spatial joins between datasets, dissolving boundaries, calculating areas/distances in projected CRS, reprojecting coordinate systems, creating choropleth maps, converting between spatial file formats, PostGIS database integration, and geospatial data analysis workflows
- **Matplotlib** - Comprehensive Python plotting library for creating publication-quality static, animated, and interactive visualizations. Provides extensive customization options for creating figures, subplots, axes, and annotations. Key features include: support for multiple plot types (line, scatter, bar, histogram, contour, 3D, and many more), extensive customization (colors, fonts, styles, layouts), multiple backends (PNG, PDF, SVG, interactive backends), LaTeX integration for mathematical notation, and integration with NumPy and pandas. Includes specialized modules (pyplot for MATLAB-like interface, artist layer for fine-grained control, backend layer for rendering). Supports complex multi-panel figures, color maps, legends, and annotations. Use cases: scientific figure creation, data visualization, exploratory data analysis, publication graphics, and any application requiring high-quality plots
- **NetworkX** - Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs. Supports four graph types (Graph, DiGraph, MultiGraph, MultiDiGraph) with nodes as any hashable objects and rich edge attributes. Provides 100+ algorithms including shortest paths (Dijkstra, Bellman-Ford, A*), centrality measures (degree, betweenness, closeness, eigenvector, PageRank), clustering (coefficients, triangles, transitivity), community detection (modularity-based, label propagation, Girvan-Newman), connectivity analysis (components, cuts, flows), tree algorithms (MST, spanning trees), matching, graph coloring, isomorphism, and traversal (DFS, BFS). Includes 50+ graph generators for classic (complete, cycle, wheel), random (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, stochastic block model), lattice (grid, hexagonal, hypercube), and specialized networks. Supports I/O across formats (edge lists, GraphML, GML, JSON, Pajek, GEXF, DOT) with Pandas/NumPy/SciPy integration. Visualization capabilities include 8+ layout algorithms (spring/force-directed, circular, spectral, Kamada-Kawai), customizable node/edge appearance, interactive visualizations with Plotly/PyVis, and publication-quality figure generation. Use cases: social network analysis, biological networks (protein-protein interactions, gene regulatory networks, metabolic pathways), transportation systems, citation networks, knowledge graphs, web structure analysis, infrastructure networks, and any domain involving pairwise relationships requiring structural analysis or graph-based modeling
- **Plotly** - Interactive scientific and statistical data visualization library for Python with 40+ chart types. Provides both high-level API (Plotly Express) for quick visualizations and low-level API (graph objects) for fine-grained control. Key features include: comprehensive chart types (scatter, line, bar, histogram, box, violin, heatmap, contour, 3D plots, geographic maps, financial charts, statistical distributions, hierarchical charts), interactive features (hover tooltips, pan/zoom, legend toggling, animations, rangesliders, buttons/dropdowns), publication-quality output (static images in PNG/PDF/SVG via Kaleido, interactive HTML with embeddable figures), extensive customization (templates, themes, color scales, fonts, layouts, annotations, shapes), subplot support (multi-plot figures with shared axes), and Dash integration for building analytical web applications. Plotly Express offers one-line creation of complex visualizations with automatic color encoding, faceting, and trendlines. Graph objects provide precise control for specialized visualizations (candlestick charts, 3D surfaces, sankey diagrams, gauge charts). Supports pandas DataFrames, NumPy arrays, and various data formats. Use cases: scientific data visualization, statistical analysis, financial charting, interactive dashboards, publication figures, exploratory data analysis, and any application requiring interactive or publication-quality visualizations
- **Polars** - High-performance DataFrame library written in Rust with Python bindings, designed for fast data manipulation and analysis. Provides lazy evaluation for query optimization, efficient memory usage, and parallel processing. Key features include: DataFrame operations (filtering, grouping, joining, aggregations), support for large datasets (larger than RAM), integration with pandas and NumPy, expression API for complex transformations, and support for multiple data formats (CSV, Parquet, JSON, Excel, Arrow). Features query optimization through lazy evaluation, automatic parallelization, and efficient memory management. Often 5-30x faster than pandas for many operations. Use cases: large-scale data processing, ETL pipelines, data analysis workflows, and high-performance data manipulation tasks
- **Seaborn** - Statistical data visualization with dataset-oriented interface, automatic confidence intervals, publication-quality themes, colorblind-safe palettes, and comprehensive support for exploratory analysis, distribution comparisons, correlation matrices, regression plots, and multi-panel figures
- **Vaex** - High-performance Python library for lazy, out-of-core DataFrames to process and visualize tabular datasets larger than available RAM. Processes over a billion rows per second through memory-mapped files (HDF5, Apache Arrow), lazy evaluation, and virtual columns (zero memory overhead). Provides instant file opening, efficient aggregations across billions of rows, interactive visualizations without sampling, machine learning pipelines with transformers (scalers, encoders, PCA), and seamless integration with pandas/NumPy/Arrow. Includes comprehensive ML framework (vaex.ml) with feature scaling, categorical encoding, dimensionality reduction, and integration with scikit-learn/XGBoost/LightGBM/CatBoost. Supports distributed computing via Dask, asynchronous operations, and state management for production deployment. Use cases: processing gigabyte to terabyte datasets, fast statistical aggregations on massive data, visualizing billion-row datasets, ML pipelines on big data, converting between data formats, and working with astronomical, financial, or scientific large-scale datasets

### Phylogenetics & Evolutionary Biology
- **ETE Toolkit** - Python library for phylogenetic tree manipulation, visualization, and analysis. Provides comprehensive tools for working with phylogenetic trees including tree construction, manipulation (pruning, collapsing, rooting), tree comparison (Robinson-Foulds distance, tree reconciliation), annotation (node colors, labels, branch styles), and publication-quality visualization. Key features include: support for multiple tree formats (Newick, Nexus, PhyloXML), integration with phylogenetic software (PhyML, RAxML, FastTree), tree annotation with metadata, interactive tree visualization, and export to various image formats (PNG, PDF, SVG). Supports species trees, gene trees, and reconciliation analysis. Use cases: phylogenetic analysis, tree visualization, evolutionary biology research, comparative genomics, and teaching phylogenetics
- **Phylogenetics** - Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. Use for evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies

### Multi-omics & AI Agent Frameworks
- **Denario** - Multiagent AI system for scientific research assistance that automates complete research workflows from data analysis through publication. Built on AG2 and LangGraph frameworks, orchestrates specialized agents for hypothesis generation, methodology development, computational analysis, and LaTeX paper writing. Supports multiple LLM providers (Google Vertex AI, OpenAI) with flexible pipeline stages allowing manual or automated inputs. Key features include: end-to-end research automation (data description → idea generation → methodology → results → paper), journal-specific formatting (APS and others), GUI interface via Streamlit, Docker deployment with LaTeX environment, reproducible research with version-controlled outputs, literature search integration, and integration with scientific Python stack (pandas, sklearn, scipy). Provides both programmatic Python API and web-based interface. Use cases: automated hypothesis generation from datasets, research methodology development, computational experiment execution with visualization, publication-ready manuscript generation, time-series analysis research, machine learning experiment automation, and accelerating the complete scientific research lifecycle from ideation to publication
- **HypoGeniC** - Automated hypothesis generation and testing using large language models to accelerate scientific discovery. Provides three frameworks: HypoGeniC (data-driven hypothesis generation from observational data), HypoRefine (synergistic approach combining literature insights with empirical patterns through an agentic system), and Union methods (mechanistic combination of literature and data-driven hypotheses). Features iterative refinement that improves hypotheses by learning from challenging examples, Redis caching for API cost reduction, and customizable YAML-based prompt templates. Includes command-line tools for generation (hypogenic_generation) and testing (hypogenic_inference). Research applications have demonstrated 14.19% accuracy improvement in AI-content detection and 7.44% in deception detection. Use cases: deception detection in reviews, AI-generated content identification, mental stress detection, exploratory research without existing literature, hypothesis-driven analysis in novel domains, and systematic exploration of competing explanations

### Scientific Communication & Publishing
- **BGPT Paper Search** - Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone
- **pyzotero** - Python client for the Zotero Web API v3. Programmatically manage Zotero reference libraries: retrieve, create, update, and delete items, collections, tags, and attachments. Export citations as BibTeX, CSL-JSON, and formatted bibliography HTML. Supports user and group libraries, local mode for offline access, paginated retrieval with `everything()`, full-text content indexing, saved search management, and file upload/download. Optional CLI and built-in MCP server (pyzotero 1.12+) for searching local Zotero 7 libraries including full-text PDF search and Semantic Scholar integration. Use cases: building research automation pipelines that integrate with Zotero, bulk importing references, exporting bibliographies programmatically, managing large reference collections, syncing library metadata, enriching bibliographic data, and connecting LLM agents to a local Zotero library.
- **Citation Management** - Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validate citations, and generate properly formatted BibTeX entries. Features include converting DOIs, PMIDs, or arXiv IDs to BibTeX, cleaning and formatting bibliography files, finding highly cited papers, checking for duplicates, and ensuring consistent citation formatting. Use cases: building bibliographies for manuscripts, verifying citation accuracy, citation deduplication, and maintaining reference databases
- **Generate Image** - AI-powered image generation and editing for scientific illustrations, schematics, and visualizations using OpenRouter's image generation models. Supports multiple models including google/gemini-3-pro-image-preview (high quality, recommended default) and black-forest-labs/flux.2-pro (fast, high quality). Key features include: text-to-image generation from detailed prompts, image editing capabilities (modify existing images with natural language instructions), automatic base64 encoding/decoding, PNG output with configurable paths, and comprehensive error handling. Requires OpenRouter API key (via .env file or environment variable). Use cases: generating scientific diagrams and illustrations, creating publication-quality figures, editing existing images (changing colors, adding elements, removing backgrounds), producing schematics for papers and presentations, visualizing experimental setups, creating graphical abstracts, and generating conceptual illustrations for scientific communication
- **Infographics** - Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes
- **LaTeX Posters** - Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication with layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices. Features compliance with conference size requirements (A0, A1, 36×48"), complex multi-column layouts, and integration of figures, tables, equations, and citations. Use cases: conference poster sessions, thesis defenses, symposia presentations, and research group templates
- **Market Research Reports** - Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix. Use cases: investment decisions, strategic planning, competitive landscape analysis, market sizing, and market entry evaluation
- **Paper-2-Web** - Autonomous pipeline for transforming academic papers into multiple promotional formats using the Paper2All system. Converts LaTeX or PDF papers into: (1) Paper2Web - interactive, layout-aware academic homepages with responsive design, interactive figures, and mobile support; (2) Paper2Video - professional presentation videos with slides, narration, cursor movements, and optional talking-head generation using Hallo2; (3) Paper2Poster - print-ready conference posters with custom dimensions, professional layouts, and institution branding. Supports GPT-4/GPT-4.1 models, batch processing, QR code generation, multi-language content, and quality assessment metrics. Use cases: conference materials, video abstracts, preprint enhancement, research promotion, poster sessions, and academic website creation
- **PPTX Posters** - Create professional research posters using PowerPoint/HTML formats for researchers who prefer WYSIWYG tools over LaTeX. Features design principles, layout templates, quality checklists, and export guidance for poster sessions. Use cases: conference posters when LaTeX is not preferred, quick poster creation, and collaborative poster design
- **Scientific Schematics** - Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review with document-type-specific thresholds (journal: 8.5/10, conference: 8.0/10, poster: 7.0/10). Specializes in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations. Features natural language input, automatic quality assessment, and publication-ready output. Use cases: creating figures for papers, generating workflow diagrams, visualizing experimental designs, and producing graphical abstracts
- **Scientific Slides** - Build slide decks and presentations for research talks using PowerPoint and LaTeX Beamer. Features slide structure, design templates, timing guidance, and visual validation. Emphasizes visual engagement with minimal text, research-backed content with proper citations, and story-driven narrative. Use cases: conference presentations, academic seminars, thesis defenses, grant pitches, and professional talks
- **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). Provides ready-to-use templates and detailed specifications for successful academic submissions. Use cases: manuscript preparation, conference papers, research posters, and grant proposals with venue-specific formatting

### Document Processing & Conversion
- **DOCX** - Create, read, edit, and manipulate Word documents (.docx files). Supports professional documents with formatting like tables of contents, headings, page numbers, letterheads, find-and-replace, tracked changes, comments, and image insertion. Use for reports, memos, letters, templates, and any Word document deliverable
- **MarkItDown** - Python utility for converting 20+ file formats to Markdown optimized for LLM processing. Converts Office documents (PDF, DOCX, PPTX, XLSX), images with OCR, audio with transcription, web content (HTML, YouTube transcripts, EPUB), and structured data (CSV, JSON, XML) while preserving document structure (headings, lists, tables, hyperlinks). Key features include: Azure Document Intelligence integration for enhanced PDF table extraction, LLM-powered image descriptions using GPT-4o, batch processing with ZIP archive support, modular installation for specific formats, streaming approach without temporary files, and plugin system for custom converters. Supports Python 3.10+. Use cases: preparing documents for RAG systems, extracting text from PDFs and Office files, transcribing audio to text, performing OCR on images and scanned documents, converting YouTube videos to searchable text, processing HTML and EPUB books, converting structured data to readable format, document analysis pipelines, and LLM training data preparation
- **LiteParse** - Fast, local-first document parser (Rust core, Python/Node bindings) for layout-aware text extraction with bounding boxes—no cloud API required. Parses PDFs natively; converts Office and image formats via LibreOffice/ImageMagick when installed. Outputs layout-preserved plain text or structured JSON with per-page `text_items` (coordinates, font metadata, OCR confidence). Built-in Tesseract OCR with optional HTTP OCR servers (EasyOCR/PaddleOCR-compatible API), page subsets, encrypted PDFs, stdin/bytes parsing, and PNG page screenshots for multimodal agents. CLI (`lit parse`, `lit batch-parse`, `lit screenshot`) and Python API (`LiteParse`, `search_items`). Targets liteparse 2.0.0, Python 3.10+. Use when you need spatial grounding for RAG, batch literature ingestion, or agent vision—not for Markdown (MarkItDown) or PDF merge/split/forms (pdf skill)
- **Markdown & Mermaid Writing** - Comprehensive markdown and Mermaid diagram writing skill for creating scientific documents, reports, analyses, and visualizations. Establishes text-based diagrams as the default documentation standard with full style guides, 24 diagram type references, and 9 document templates
- **PDF** - Read, create, combine, split, rotate, watermark, encrypt/decrypt, and manipulate PDF files. Supports extracting text/tables, filling forms, OCR on scanned PDFs, image extraction, and format conversion
- **PPTX** - Create, read, edit, and manipulate PowerPoint presentations (.pptx files). Use for slide decks, pitch decks, extracting text from presentations, editing existing slides, combining or splitting presentations, and working with templates, layouts, speaker notes, and comments
- **XLSX** - Spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization

### Laboratory Automation & Equipment Control
- **PyLabRobot** - Hardware-agnostic, pure Python SDK for automated and autonomous laboratories. Provides unified interface for controlling liquid handling robots (Hamilton STAR/STARlet, Opentrons OT-2, Tecan EVO), plate readers (BMG CLARIOstar), heater shakers, incubators, centrifuges, pumps, and scales. Key features include: modular resource management system for plates, tips, and containers with hierarchical deck layouts and JSON serialization; comprehensive liquid handling operations (aspirate, dispense, transfer, serial dilutions, plate replication) with automatic tip and volume tracking; backend abstraction enabling hardware-agnostic protocols that work across different robots; ChatterboxBackend for protocol simulation and testing without hardware; browser-based visualizer for real-time 3D deck state visualization; cross-platform support (Windows, macOS, Linux, Raspberry Pi); and integration capabilities for multi-device workflows combining liquid handlers, analytical equipment, and material handling devices. Use cases: automated sample preparation, high-throughput screening, serial dilution protocols, plate reading workflows, laboratory protocol development and validation, robotic liquid handling automation, and reproducible laboratory automation with state tracking and persistence

### Tool Discovery & Computational Resources
- **Get Available Resources** - Detect available computational resources and generate strategic recommendations for scientific computing tasks at the start of any computationally intensive scientific task. Automatically identifies CPU capabilities, GPU availability (NVIDIA CUDA, AMD ROCm, Apple Silicon Metal), memory constraints, and disk space. Creates JSON file with resource information and recommendations for parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use cases: determining optimal computational approaches before data analysis, model training, or large file operations

### Research Methodology & Proposal Writing
- **Paperzilla** - Chat with your agent about Paperzilla projects, recommendations, and canonical papers. Use for recent project recommendations, recommendation triage, canonical paper details, markdown-based summaries, relevance-to-my-research discussions, recommendation feedback, JSON export, and Atom feed URLs
- **Paper Lookup** - Search 10 academic paper databases via their REST APIs to find research papers, preprints, and scholarly articles. Covers biomedical literature (PubMed, PMC full text), preprint servers (bioRxiv, medRxiv, arXiv), multidisciplinary indexes (OpenAlex, Crossref, Semantic Scholar), open access aggregators (CORE, Unpaywall). Use for searching research papers, finding citations, looking up articles by DOI or PMID, retrieving abstracts or full text, checking open access availability, exploring citation graphs, and systematic literature searches
- **Research Grants** - Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Features agency-specific formatting, review criteria understanding, budget preparation, broader impacts statements, significance narratives, innovation sections, and compliance with submission requirements (including PAPPG 24-1 and current NIH salary-cap guidance). Covers project descriptions, specific aims, technical narratives, milestone plans, budget justifications, and biosketches. Optional figures via the scientific-schematics skill. Use cases: federal grant applications, resubmissions with reviewer response, multi-institutional collaborations, and preliminary data sections
- **Research Lookup** - Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Intelligently selects models based on query complexity. Provides access to current academic literature, recent studies, technical documentation, and general research information with proper citations. Use cases: finding latest research, literature verification, gathering background research, finding citation sources, and staying current with emerging trends
- **Scholar Evaluation** - Apply the ScholarEval framework to systematically evaluate scholarly and research work. Provides structured evaluation methodology based on peer-reviewed research assessment criteria for analyzing academic papers, research proposals, literature reviews, and scholarly writing across multiple quality dimensions. Use cases: evaluating research papers for quality and rigor, assessing methodology design, scoring data analysis approaches, benchmarking research quality, and assessing publication readiness

### Regulatory & Standards Compliance
- **ISO 13485 Certification** - Comprehensive toolkit for preparing ISO 13485:2016 certification documentation for medical device Quality Management Systems. Provides gap analysis of existing documentation, templates for all mandatory documents, compliance checklists, and step-by-step documentation creation. Covers 31 required procedures including Quality Manuals, Medical Device Files, and work instructions. Use cases: starting ISO 13485 certification process, conducting gap analysis, creating or updating QMS documentation, preparing for certification audits, transitioning from FDA QSR to QMSR, and harmonizing with EU MDR requirements

## Scientific Thinking & Analysis

### Analysis & Methodology
- **Exploratory Data Analysis** - Comprehensive EDA toolkit with automated statistics, visualizations, and insights for any tabular dataset
- **Hypothesis Generation** - Structured frameworks for generating and evaluating scientific hypotheses
- **Literature Review** - Systematic literature search and review toolkit with support for multiple scientific databases (PubMed, bioRxiv, Google Scholar), citation management with multiple citation styles (APA, AMA, Vancouver, Chicago, IEEE, Nature, Science), citation verification and deduplication, search strategies (Boolean operators, MeSH terms, field tags), PDF report generation with formatted references, and comprehensive templates for conducting systematic reviews following PRISMA guidelines
- **Peer Review** - Comprehensive toolkit for conducting high-quality scientific peer review with structured evaluation of methodology, statistics, reproducibility, ethics, and presentation across all scientific disciplines
- **Scientific Brainstorming** - Conversational brainstorming partner for generating novel research ideas, exploring connections, challenging assumptions, and developing creative approaches through structured ideation workflows
- **Scientific Critical Thinking** - Tools and approaches for rigorous scientific reasoning and evaluation
- **Scientific Visualization** - Best practices and templates for creating publication-quality scientific figures with matplotlib and seaborn, including statistical plots with automatic confidence intervals, colorblind-safe palettes, multi-panel figures, heatmaps, and journal-specific formatting
- **Scientific Writing** - Comprehensive toolkit for writing, structuring, and formatting scientific research papers using IMRAD format, multiple citation styles (APA, AMA, Vancouver, Chicago, IEEE), reporting guidelines (CONSORT, STROBE, PRISMA), effective figures and tables, field-specific terminology, venue-specific structure expectations, and core writing principles for clarity, conciseness, and accuracy across all scientific disciplines
- **Statistical Analysis** - Guided hypothesis testing, assumption checks, effect sizes, power analysis, and APA reporting (Pingouin, SciPy, statsmodels, PyMC). For dedicated model APIs see statsmodels and pymc skills

### Decision & Scenario Analysis
- **Consciousness Council** - Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use for diverse viewpoints, tough decisions, devil's advocate analysis, exploring problems from multiple angles, or when facing dilemmas, trade-offs, and complex choices with no obvious answer
- **DHDNA Profiler** - Extract cognitive patterns and thinking fingerprints from any text. Analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, and gain deeper insight into an author's reasoning patterns, decision-making style, or cognitive signature
- **What-If Oracle** - Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card). Use for speculative what-if questions, strategic forks, contingency planning, and stress-testing decisions before committing

### Web Search & Information Retrieval
- **Exa Search** - Web search and URL content extraction via the Exa API. Use for high-quality web search tuned for scientific and technical content, scholarly filtering via `category="research paper"` plus academic domain allowlists, and batch URL extraction
- **Parallel Web** - Search the web, extract URL content, and run deep research using the Parallel Chat API and Extract API. Use for web searches, research queries, and general information gathering with synthesized summaries and citations
