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 BioCyc.org 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.

• BioCyc overview (11:15) [mp4 video] or [YouTube]
• Searching in BioCyc (15:15) [mp4 video] or [YouTube]
• Genes, Operons, Genome Browser, Sequence (14:19) [mp4 video] or [YouTube]
• Pathways (15:11) [mp4 video] or [YouTube]
• Reactions (3:51) [mp4 video] or [YouTube]
• Compounds (5:48) [mp4 video] or [YouTube]

Webinar #2: 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 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.

• Quick Introduction (6:27): "Structured Advanced Query Page Quick Introduction" [Windows Media Video] or [mp4 video]
• Full Webinar (42:15): "Structured Advanced Query Page" [Windows Media Video] or [mp4 video]

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 BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms. In this webinar, you'll learn about:

• Using the Cellular Overview to browse an organism's metabolic network, and to view gene expression, proteomics, and metabolomics datasets
• Comparative operations for genome and metabolic data in BioCyc
• All about orthologs in BioCyc
• Using the Regulatory Overview to browse a cell's transcriptional regulatory network

"Comparative and Omics Tools in BioCyc" is presented in five separate files. To download or view, click on one of the links following each segment's name.

• Part 1: The Cellular Overview: Navigating metabolic networks (17:15) [mp4 video] or [QuickTime Video] or [YouTube]
• Part 2: The Cellular Omics Viewer (25:08) [mp4 video] or [QuickTime Video] or [YouTube]
• Part 3: Comparative Genomics (21:06) [Windows Media Video] or [QuickTime Video]
• Part 4: Ortholog Viewing (10:02) [Windows Media Video] or [QuickTime Video]
• Part 5: The Regulatory Overview (15:15) [mp4 video] or [QuickTime Video] or [YouTube]

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

• Part 1: Building the Database (56:42) [Windows Media Video] or [QuickTime Video]
• Part 2A: General Editing Strategies (8:00) [Windows Media Video] or [QuickTime Video]
• Part 2B: Creating and Editing Reactions and Compounds (17:32) [Windows Media Video] or [QuickTime Video]
• Part 2C: Working With Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [Windows Media Video] or [QuickTime Video]
• Part 2D: Making and Editing Pathways (9:42) [Windows Media Video] or [QuickTime Video]

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.

• Part 1: SmartTables Overview (2:27) [QuickTime Video]
• Part 2: SmartTables Basics (12:43) Updated! [QuickTime Video]
• Part 3: SmartTables Transformations (8:08) Updated! [QuickTime Video]
• Part 4: SmartTables Import and Export (9:00) Updated! [QuickTime Video]
• Part 5: SmartTables Gene Expression Analysis (7:40)Updated! [QuickTime Video]
• Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video]

Webinar #6: Pathway Collages

This webinar will show you how to use the Pathway Collage Viewer to generate, customize and export high-quality diagrams showing collections of user-specified pathways.

• Pathway Collages (22:39) [mp4 video], [QuickTime Video] or [YouTube]

Webinar #7: Omics Dashboard

This webinar will show you how to use the Omics Dashboard, a new tool for visualizing omics data.

• Omics Dashboard Part 1 (16:35) [mp4 video], [QuickTime Video] or [YouTube]
• Omics Dashboard Part 2 (24:29) [mp4 video], [QuickTime Video] or [YouTube]