This project is a collection of specialized toolkits and an agent skill library designed to equip large language model agents with the capabilities to perform complex scientific research across biology, chemistry, medicine, and physics. It provides a structured framework of integration paths and tools that allow agents to execute multi-step research workflows. The system is distinguished by its domain-specific toolsets, including a bioinformatics toolkit for genomic and single-cell analysis, a cheminformatics toolset for drug-target binding and lead compound optimization, and a multi-omics an
Biopython is a bioinformatics library for Python providing tools to parse, manipulate, and analyze biological sequences, molecular structures, and phylogenetic trees. It serves as a biological sequence parser for genomic and proteomic data across multiple industry-standard file formats and acts as an interface for querying biological data and citations from NCBI Entrez repositories. The project distinguishes itself through specialized toolkits for protein structure analysis and phylogenetic tree construction. It includes a protein structure analyzer for processing PDB and mmCIF files to calcu
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
The main features of oschwengers/bakta are: Genome Annotation.
Open-source alternatives to oschwengers/bakta include: k-dense-ai/scientific-agent-skills — This project is a collection of specialized toolkits and an agent skill library designed to equip large language model… biopython/biopython — Biopython is a bioinformatics library for Python providing tools to parse, manipulate, and analyze biological… tseemann/prokka — :zap: :aquarius: Rapid prokaryotic genome annotation.
