Introduction to BioCyc for New Life Sciences Graduate Students and Post-Docs

BioCyc will be presenting a series of Zoom presentations designed to introduce new graduate students in the life sciences to the most important features of the BioCyc website ( Each tutorial will run about an hour and start at 9:00AM US Pacific time (12:00PM US Eastern time). We will be monitoring chat during each session and will answer as many questions as possible during the session or afterwards as time allows.

Please forward this announcement to a graduate program administrator and/or students and post-docs at your institution.

BioCyc Overview is an extensive web portal containing 19,000 genomes and associated metabolic pathways for microbes, model eukaryotes, and humans. The BioCyc website provides extensive bioinformatics tools for searching and analyzing these databases, and leveraging them for analysis of omics datasets.

BioCyc databases combine curated information with data imported from multiple sources, and with computationally inferred data (metabolic pathways, operons, PFam domains, and orthologs). Curated databases receive intensive review and updating by a Ph.D. biologist that includes reviewing the computationally predicted metabolic pathways, entering new gene functions and metabolic pathways from the experimental literature, defining regulatory relationships, and creating protein complexes. Overall the BioCyc databases have been curated from 130,000 publications.

BioCyc genome-related tools include a genome browser, sequence searching and alignment, and extraction of sequence regions. 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, as well as showing full organism regulatory networks. Comparative analysis tools enable comparisons of genome organization, of orthologs, and of pathway complements. Omics data analysis tools support enrichment analysis and painting of transcriptomics and metabolomics data onto individual pathway diagrams and onto zoomable metabolic map diagrams. The Omics Dashboard tool enables interactive exploration of omics datasets through a hierachy of cellular systems.


We will cover the following topics in each presentation:

Introduction to BioCyc - November 3 at 12pm US Eastern Daylight Time

Topics include:

SmartTables and Comparative Analysis - November 10 at 12pm US Eastern Standard Time

Non-US attendees, please note that this is an hour later than the previous week. Topics include:

Transcriptomics and Metabolomics Data Analysis - November 17 at 12pm US Eastern Standard Time

Topics include:


Registration is required, but free. We are using Zoom Webinars for registration, you can register here.