Tutorial for the BioCyc.org Genome and Metabolic Pathway Web Portal

The BioCyc.org web portal contains 20,000 genomes and associated metabolic pathways for microbes, model eukaryotes, and humans. BioCyc provides extensive bioinformatics tools for search and analysis.

BioCyc databases combine curated information with data imported from multiple sources, and with computationally inferred data (metabolic pathways, operons, and orthologs). Curated databases receive intensive review and updating by Ph.D. biologists that includes entering new gene functions and metabolic pathways from the experimental literature and defining regulatory relationships. 75 BioCyc databases have been curated from 153,000 publications.

BioCyc includes a high-speed genome browser with a comparative mode. Pathway-related tools include pathway diagrams, a tool for navigating zoomable organism-specific metabolic map diagrams, and a tool for searching for metabolic routes that transform a starting metabolite into a product metabolite.

Regulation tools depict operons and regulatory sites, and show full organism regulatory networks. Omics data analysis tools support enrichment analysis and painting of transcriptomics and metabolomics data onto individual pathway diagrams and onto zoomable metabolic map diagrams.