BioCyc Webinars

Webinars on Demand: Download Webinar Videos

The BioCyc on Demand Webinar series introduces basic and advanced features of the BioCyc website and the Pathway Tools software system via a combination of narration and practical demonstration. Webinar videos can be downloaded directly from the links on this page.

Webinar #1: Introduction to BioCyc

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

"Introduction to BioCyc" is presented here in six sequential segments, giving you a guided tour of the BioCyc collection in concise bites. To download or view, just click on one of the links following each segment's name.

Webinar #2: Introduction to SmartTables

The following webinar will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The webinar is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below.

Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network

This webinar 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.

Webinar #4: Omics Data Analysis

This webinar will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.

Webinar #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 webinar will show you how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways.

Webinar #6: Creating a Pathway/Genome Database

This webinar 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:

Webinar #7: Using the Structured Advanced Query Page

The "Using the Structured Advanced Query Page" webinar introduces users to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. In this webinar, you'll learn about:

  • 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

To download or view, click one of the links below.

Recordings from Live BioCyc Webinars

 We have been conducting tutorials and other special webinars on Zoom since 2021. We record many of these and make them available here.
  • Introduction to BioCyc for new Students and PostDocs.
    • Part 1, Presented by Peter Karp, November 3, 2021. YouTube or mp4
    • Part 2, Presented by Peter Midford, November 10, 2021. YouTube or mp4
    • Part 3, Presented by Suzanne Paley, November 17, 2021. YouTube or mp4

  • PGDB Editing Tutorial, presented by Ron Caspi.

  • Helicobacter pylori Webinar, presented by Ron Caspi, March 17, 2022. mp4

  • Introduction to Pathway Tools Webinar, presented by Peter Karp, April 5, 2022. mp4

  • Pathway Tools Computational Inferences Webinar, presented by Peter Karp, April 12, 2022. mp4