Skill UI

Biopython provides Python APIs for sequence manipulation, database access, BLAST automation, structural bioinformatics, and phylogenetics, making it ideal for scripting custom pipelines and batch processing in computational molecular biology workflows.

BioServices provides Python wrappers for 40+ bioinformatics services, allowing cross-database queries, identifier mapping, pathway exploration, and sequence or compound research within consistent workflows.

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

gget is a CLI/Python client that unifies querying over 20+ bioinformatics databases, letting researchers fetch gene info, sequences, BLAST results, structures, and enrichment data interactively or within scripts.

LatchBio Integration provides a Python-first platform to compose, deploy, and monitor serverless bioinformatics pipelines with the Latch SDK, decorator-based tasks, cloud storage (LatchFile/Dir), GPU tuning, and Nextflow or Snakemake interoperability.

scikit-bio provides a Python-native biological data toolkit for reading/writing FASTA/Newick files, manipulating sequences, building alignments and phylogenies, and calculating diversity metrics for microbiome and ecology workflows.

polars-bio accelerates genomic interval math and bioinformatics I/O by combining Polars, Arrow, and DataFusion to handle BED/VCF/BAM/GFF/FASTA streams, SQL queries, and cloud storage with overlap, coverage, and nearest APIs plus streaming fallbacks.

Provides direct REST API access to UniProt, the premier resource for protein sequence and functional information. This skill enables users to search proteins by name, gene, or accession number, retrieve sequences in FASTA format, perform cross-database ID mapping (e.g., Ensembl, RefSeq), and analyze functional annotations (GO terms) for building comprehensive bioinformatics pipelines.

AnnData is a specialized Python package designed for managing and analyzing annotated matrices, particularly crucial in single-cell genomics and bioinformatics. It efficiently stores experimental measurements (X) alongside comprehensive metadata (obs, var, obsm, etc.). This skill allows users to read, write, subset, and concatenate large, complex datasets in formats like .h5ad and .zarr, making it essential for scRNA-seq analysis workflows and integration with the scverse ecosystem.

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.