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.
Make the most of BioCyc! The "Introduction to BioCyc" Tutorial introduces you to the BioCyc.org site and to the BioCyc collection of thousands of Pathway/Genome Databases.
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.
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.
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.
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:
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.