Skill UI

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.

A comprehensive Python package providing a unified interface to over 40 major bioinformatics web services and databases. Use it for complex biological workflows, including cross-database querying (e.g., UniProt, KEGG, ChEMBL), identifier mapping, protein sequence retrieval, pathway analysis, and running sequence similarity searches like BLAST. It streamlines data integration from multiple life science resources into consistent Python code.

Provides programmatic access to massive, versioned public single-cell and spatial transcriptomics datasets from CZ CELLxGENE. This skill allows users to efficiently query specific subsets of cell metadata, gene expression matrices, embeddings, and summary statistics across various organisms, tissues, and diseases. It is ideal for large-scale, memory-efficient biological research and model training without full dataset downloads.

gget is a comprehensive command-line tool and Python package offering unified access to over 20 genomic databases. It facilitates quick lookups for gene information, sequence analysis (BLAST), protein structures, and expression data, supporting both interactive CLI use and advanced programmatic Python workflows for biological research.

LaminDB is an open-source, lineage-native lakehouse specifically designed for complex biological datasets and models. It provides unified capabilities for querying, tracking data lineage, validating schemas, and ensuring FAIR compliance across diverse data types (e.g., AnnData, Parquet, Zarr). Use this skill when managing multi-modal genomic data, tracking computational workflows (like Nextflow/Snakemake), or building robust, reproducible data infrastructure in bioinformatics.

Perform comprehensive molecular dynamics (MD) simulations using high-performance engines like OpenMM and analysis tools like MDAnalysis. This skill allows users to model the time evolution of biological systems, covering system preparation (solvation, force field assignment), energy minimization, NVT equilibration, and advanced analysis (RMSD, free energy surfaces). Ideal for structural biology, drug binding studies, and biophysics research.

NeuroKit2 is a comprehensive Python toolkit designed for processing and analyzing diverse physiological biosignals. It covers multiple domains including cardiovascular (ECG, PPG), neural (EEG), autonomic (EDA), respiratory (RSP), and muscular (EMG) signals. Use this skill for advanced psychophysiology research, complex pattern detection, and real-time clinical monitoring applications.

This skill provides a comprehensive Python API integration for the OMERO platform, an open-source solution for managing and analyzing large-scale microscopy datasets. Users can programmatically access images, retrieve structured data, analyze raw pixel data, manage complex annotations (ROIs), and execute batch processing workflows essential for high-content screening and advanced biological research.

This comprehensive skill provides a standardized pipeline for reconstructing the evolutionary history of biological sequences (genes, proteins, genomes). It guides users through essential steps, including multiple sequence alignment using MAFFT, maximum likelihood tree inference with IQ-TREE 2, and visualization with ETE3. Ideal for research in viral phylodynamics, molecular clock studies, and large-scale comparative genomics.

This skill provides programmatic access to the PrimeKG, a comprehensive knowledge graph integrating over 20 primary databases. It facilitates multiscale biological research by mapping complex relationships between genes, drugs, diseases, and phenotypes. Use it for drug repurposing, identifying novel disease targets, and analyzing molecular mechanisms across various biological scales.

PyHealth is a comprehensive Python toolkit designed for building deep-learning pipelines in the clinical and healthcare domains. It supports diverse data modalities, including EHR records, physiological signals, and medical images. The framework follows a stable 5-stage pipeline (Dataset → Task → Model → Trainer → Metrics), enabling users to perform complex tasks like predicting mortality, optimizing drug recommendations, staging sleep, or cross-mapping medical codes (ICD/ATC/RxNorm) on datasets like MIMIC-III/IV and OMOP.

scikit-bio is a comprehensive Python library designed for advanced bioinformatics and biological data analysis. It provides robust capabilities for sequence manipulation (DNA, RNA, Protein), performing complex sequence alignments (pairwise and multiple), constructing and analyzing phylogenetic trees, and calculating diverse ecological metrics. It is essential for microbiome analysis, evolutionary studies, and general biological data processing, supporting standard formats like FASTA, Newick, and BIOM.