BioCyc Online Tutorials
Introduction to BioCyc for New Users
What Can I Do with BioCyc? 2-Minute Tutorials
Each 2-minute tutorial introduces a key area of BioCyc functionality in two minutes or less.
- Find information about a gene
- Find information about a metabolite or a metabolic pathway
- Genome Browser
- Extract the sequence of a gene, a protein, or of a chromosomal region
- Find all proteins in an organism containing a given sequence pattern
- Produce a multiple sequence alignment
- Search for genes or proteins via multiple criteria
- Navigate through the metabolic network of an organism
- Compare information about a list of known genes (via SmartTables)
- Compare the metabolic potentials of several organisms
- Analyze transcriptomics and metabolomics data
- Comparative Genome Alignments
In-Depth BioCyc Tutorials on YouTube
These BioCyc tutorials present both basic and advanced features of the BioCyc website and the Pathway Tools software system via a combination of narration and practical demonstration. To access a tutorial, click the left triangle to list the tutorial segments.
- Part 1A: Introduction to Database Building and Pathologic (14:04)
- Part 1B: Building a Database: Detailed Pathologic Example (23:53)
- Part 2A: General Editing Strategies (8:00)
- Part 2B: Creating and Editing Reactions and Compounds (17:32)
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10)
- Part 2D: Making and Editing Pathways (9:42)
- The basic steps of setting up an advanced query
- Four examples of increasingly complex queries, including how to query across multiple databases
- Where to learn more about the structure of BioCyc databases
Tutorial #1: Introduction to BioCyc
Tutorial #2: Introduction to SmartTables
The following Tutorial will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To view, click one of the links below.
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This Tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
Tutorial #4: Omics Data Analysis
Tutorial #5: Pathway Collages
Pathway collages are multi-pathway diagrams that you can customize in various respects, such as overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. This Tutorial will show you how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways.
Tutorial #6: Creating a Pathway/Genome Database
This Tutorial walks you through the process of building a BioCyc-like Pathway/Genome Database (PGDB) for an organism with a sequenced and annotated genome. Learn how to predict metabolic pathways and operons, how to revise gene and protein annotations, build metabolic pathways, make protein complexes, add metabolic reactions and compounds, and assign Gene Ontology (GO) terms to genes. Build a PGDB for your own lab or for the whole scientific community. Segments:
Tutorial #7: Using the Structured Advanced Query Page
The Structured Advanced Query Page enables construction of complex queries to PGDBs, and queries across one or more databases in the BioCyc collection. In this Tutorial, you'll learn about:
To view, click one of the links below.
Coursera Course on Pathway Bioinformatics
An online course on pathway bioinformatics by Peter Karp is available on Coursera and on Stepik (free).
Recordings from Live BioCyc Tutorials
We have been conducting tutorials and other special webinars on Zoom since 2021. We record many of these and make them available here.- Helicobacter pylori Genome Database Tutorial, presented by Ron Caspi, March 17, 2022. mp4
- "Introduction to Pathway Tools", presented by Peter Karp, April 5, 2022. mp4
- "Pathway Tools Computational Inferences", presented by Peter Karp, April 12, 2022. mp4
- "A Comparison of the BioCyc and KEGG Pathway Databases", presented by Peter Karp, June 19, 2025. Mov