Claude Scientific Skills

Generates and analyzes protein sequences and structures using ESM3, ESMC, and ESMFold2, with support for local and cloud inference.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Runs time series machine learning tasks—classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search—using the scikit-learn compatible aeon toolkit.

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

Organize, query, validate, and convert neuroscience datasets following the Brain Imaging Data Structure (BIDS) standard, including metadata sidecars and derivatives.

DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.

Design, simulate, and run quantum circuits on Google Quantum AI and partner hardware using Cirq, including noise modeling and characterization experiments.

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

Scales pandas and NumPy workflows to datasets larger than memory using parallel and distributed computing, with support for dataframes, arrays, bags, and custom task graphs.

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.

Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), reading/writing graph file formats, or drawing network topologies. Common applications include social, biological, transportation, and citation networks.

Build, fit, validate, and compare Bayesian models using PyMC, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.

Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

Explains machine learning model predictions using SHAP values, covering feature importance, visualizations, debugging, bias analysis, and production deployment.

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

Process and analyze tabular datasets larger than RAM using lazy, out-of-core DataFrames, with fast aggregations, visualization, and machine learning integration.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Runs an autonomous optimization loop that iteratively improves an artifact against an objective and evaluator using Hypothesis Tree Refinement, with subagent executors in isolated git worktrees.

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

Deploy and scale Python AI/ML workloads on Modal's serverless cloud, including GPU compute, web endpoints, scheduled jobs, and persistent storage.

Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

Solves single- and multi-objective optimization problems with NSGA-II/III, MOEA/D, and other evolutionary algorithms, including constraint handling, Pareto front analysis, and benchmark problems.

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. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

Read, write, and analyze genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch or JAX. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.

Access AI-ready drug discovery datasets, benchmarks, and molecular oracles from Therapeutics Data Commons for therapeutic machine learning and pharmacological prediction.

High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.

Simulate and analyze quantum mechanical systems, including open quantum systems, using QuTiP's solvers for master equations, Lindblad dynamics, and quantum trajectories.

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

Provides guidance for using RDKit to read and write molecular structures, calculate descriptors, generate fingerprints, perform substructure searches, and handle chemical reactions.

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Run cloud-native molecular modeling and drug-design workflows via a Python API, covering pKa prediction, docking, conformer and tautomer ensembles, molecular dynamics, and related small-molecule or protein tasks without local HPC infrastructure.

Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

Build discrete-event simulations of systems with processes, queues, resources, and time-based events using the SimPy framework in Python.

Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

Provides guidance for using SymPy for exact symbolic mathematics in Python, covering algebra, calculus, equation solving, linear algebra, physics, and code generation.

Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.

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.

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1, extracting events as NumPy arrays, metadata, and channel information, with support for creating and modifying FCS files.

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

Trains machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

Use UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows.

Numerical computing with MATLAB and GNU Octave for matrix operations, data analysis, visualization, and scientific computing, including script execution and syntax guidance.

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

Loads and processes whole-slide pathology images, builds spatial graphs, trains deep learning models, and analyzes multiplexed immunofluorescence data across 160+ slide formats.

Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.

Creates interactive, publication-quality charts with 40+ types, hover tooltips, zoom, and web-embeddable exports for dashboards and exploratory analysis.

Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.

High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.

Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.

Build, optimize, and execute quantum circuits on IBM Quantum hardware or local simulators using Qiskit, including transpilation, primitives, and algorithm libraries.

Use Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests that explicitly need current web evidence, academic-source discovery, repeated entity lookups, exhaustive reports, or ongoing change tracking.

Runs standard single-cell RNA-seq analysis with Scanpy, covering QC, normalization, dimensionality reduction, clustering, marker identification, visualization, and conversion of R single-cell formats to h5ad.

Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.

Analyze RNA velocity in single-cell RNA-seq data with scVelo, estimating cell state transitions from unspliced/spliced mRNA dynamics, inferring trajectory directions, computing latent time, and identifying driver genes.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.