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BioCyc Webinars

The BioCyc 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 this site or acquired from our podcast feed as they come out. Download a BioCyc webinar and learn more about BioCyc today.

Webinars on Demand: Download Webinar Videos

We have an expanding collection of webinar videos so that you can download, learn, and review at your own pace.

Webinar #1: Introduction to BioCyc

Make the most of BioCyc!

The "Introduction to BioCyc" webinar introduces you to the site and to the BioCyc collection of thousands of Pathway/Genome Databases. During this webinar, you'll learn about:

  • BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
  • How to search, browse, and find what you need in the BioCyc collection
  • How we represent metabolism, transcription, and all their parts

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

Webinar #2: Using the Structured Advanced Query Page

Once you've mastered the quick and intermediate searches described in the introductory webinar series, move on to the Structured Advanced Query Page and learn how to ask complex queries across one or more databases in the BioCyc collection. In this webinar, we cover:

  • The basic steps of setting up an advanced query using our structure input page
  • 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.

Webinar #3:Comparative Tools, Zoomable Metabolic Map, Omics Data Analysis

The "Comparative and Omics Tools in BioCyc" webinar introduces users to many of the advanced tools available on the website for comparing organisms and understanding large-scale experimental data. In this webinar, you'll learn about:

  • Using the Cellular Overview to examine an organism's metabolism, and to view gene expression, proteomics, and metabolomics datasets
  • How you can compare the metabolic and other features of multiple organisms in the BioCyc collection
  • All about ortholog viewing in BioCyc

Note that we have not yet updated this webinar to show off the revised BioCyc site. Although the omics and comparative tools all work basically the same way in the new site, you can now reach them much more conveniently from the "Tools" menu at the top of any page.

"Comparative and Omics Tools in BioCyc" is presented in four sequential files, leading you through the tools in a logical fashion in 10-35 minute segments. To download or view, just click on one of the links following each segment's name.

You can also download an older, single-file version of this webinar by clicking on the following link (49:00):

Webinar #4: Creating a Pathway/Genome Database

This webinar walks you through the process of building a Pathway Tools Pathway/Genome Database (PGDB) from an annotated genome file. Learn how to annotate proteins, 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. Topics include:

  • Obtaining genome files to input into Pathway Tools
  • Generating a draft database with predicted pathways, transcription units, pathway hole fillers, and more
  • Editing a PGDB, with an eye toward editing your brand-new database into the final product you want

Webinar #5: Introduction to SmartTables/Web Groups

The following webinar will guide you through SmartTables, formerly known as Web Groups, which allows you to create, upload, share, and compute with your own datasets. 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.