Systems Biology

This skill enables querying the STRING database for protein-protein interaction networks, functional enrichment analysis (GO, KEGG, Pfam), and homology comparisons. It covers 59 million proteins across 5000+ species and supports workflows like network visualization, pathway analysis, and hub protein discovery.

This skill enables querying the Reactome database for biological pathway analysis. It supports pathway enrichment analysis on gene/protein lists, expression data analysis, gene-to-pathway mapping, and visualization of results in the Reactome Pathway Browser for systems biology research.

COBRApy is a documentation skill for systems biology and metabolic engineering analysis. It provides comprehensive guidance on using the COBRApy Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, including flux balance analysis, gene knockouts, flux sampling, and SBML model handling.