Skill UI

Aeon is a comprehensive, scikit-learn compatible Python toolkit designed for advanced time series analysis. It supports a wide range of temporal machine learning tasks, including classification, regression, clustering, forecasting, anomaly detection, and similarity search. Use this skill when working with sequential patterns, time-indexed observations, or complex temporal data that requires specialized algorithms.

Astropy is the fundamental Python package for astronomical research and astrophysics data processing. It provides essential tools for handling physical units, performing coordinate transformations across celestial frames (ICRS, Galactic, etc.), managing FITS files, conducting cosmological calculations, and precise time handling. It is indispensable for any task involving celestial coordinates, unit conversions, or analyzing large astronomical catalogs.

Biopython is a robust, comprehensive toolkit for computational molecular biology written in Python. It enables users to manipulate biological sequences (DNA, RNA, protein), parse standard formats (FASTA, GenBank, PDB, etc.), and programmatically access major bioinformatics databases like NCBI via Entrez. This skill is ideal for developing complex bioinformatics pipelines, including sequence alignment, structural analysis, and phylogenetic tree construction.

COBRApy is a powerful Python library for Constraint-Based Reconstruction and Analysis (COBRA). It enables deep dives into cellular metabolism, allowing users to build, simulate, and analyze complex metabolic models (e.g., genome-scale models). Core functionalities include Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), performing gene/reaction knockouts, and optimizing growth media. It supports standard metabolic model formats like SBML, JSON, and YAML.

Datamol provides a simplified, Pythonic abstraction layer over RDKit, making complex molecular operations accessible for chemical data science. It supports core functionalities including SMILES parsing, structure standardization, calculation of molecular descriptors (e.g., LogP, MW), 3D conformer generation, and efficient parallel batch processing. It is ideal for streamlining molecular data handling in drug discovery and chemical research pipelines.

DeepChem is a comprehensive Python library designed for applying machine learning to complex fields like chemistry, materials science, and biology. It enables users to perform molecular property prediction (e.g., ADMET, toxicity), train models using specialized graph neural networks (GNNs), and process diverse molecular formats (SMILES, SDF, FASTA). It provides extensive featurization options, making it foundational for drug discovery and computational chemistry research.

This skill provides programmatic access to the Cancer Dependency Map (DepMap), a comprehensive resource characterizing genetic dependencies in cancer cell lines. Use it to identify genes essential for specific cancer types, discover synthetic lethal interactions, and validate potential oncology drug targets using CRISPR and RNAi data.

ETE is a comprehensive toolkit for phylogenomic research, designed to handle and analyze hierarchical tree structures. It supports various tree formats (Newick, NHX) and provides advanced functionalities such as detecting evolutionary events (duplication/speciation), identifying orthologs/paralogs, integrating with NCBI taxonomy for lineage tracking, and generating publication-quality visualizations in PDF/SVG.

A lightweight Python library designed for reading, parsing, and writing Flow Cytometry Standard (FCS) files. It extracts event data as NumPy arrays, handles complex metadata, and supports multiple FCS versions (2.0-3.1). Ideal for data preprocessing, building cytometry pipelines, and inspecting experimental results.

Geniml is a comprehensive Python package designed for applying machine learning models to genomic interval data, typically stored in BED files. It provides several unsupervised methods—including Region2Vec and BEDspace—to learn robust embeddings of genomic regions, single cells (scATAC-seq), and associated metadata. Use cases include dimensionality reduction, structural variation analysis, cell-type annotation, and cross-modal querying in genomics research.

A powerful Python library that extends pandas to enable complex spatial operations on vector geometric data. It supports reading and writing diverse formats, including Shapefile, GeoJSON, and GeoPackage. Users can perform advanced GIS tasks such as spatial joins, buffering, overlay analysis, calculating areas, managing Coordinate Reference Systems (CRS), and generating interactive choropleth maps, making it essential for geographic data science projects.

This skill proactively detects and reports comprehensive system resources, including CPU cores, GPU types (NVIDIA, AMD, Apple Silicon), available memory, and disk space. It generates a detailed JSON report with strategic, context-aware recommendations for optimizing scientific computing workflows, such as recommending parallel processing libraries (Dask, joblib), out-of-core methods (Zarr), or appropriate GPU acceleration backends (Metal, ROCm). Use this before any large-scale data analysis, model training, or computationally intensive simulation to make informed architectural decisions.