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.

• BioCyc Overview Part 1 (8:10) [mp4 video] or [YouTube]
• BioCyc Overview Part 2 (4:44) [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: 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.

• Part 1: SmartTables Overview (4:30) [mp4 video] or [YouTube]
• Part 2: SmartTables Basics (12:43) [QuickTime Video] or [YouTube]
• Part 3: SmartTables Transformations (8:08) [QuickTime Video] or [YouTube]
• Part 4: SmartTables Import and Export (9:00) [QuickTime Video] or [YouTube]
• Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video] or [YouTube]
• Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video] or [YouTube]

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.

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

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.

• Transcriptomics Analysis Tools [brief tour (2:40) mp4 video | YouTube] [detailed tutorial (21:36) mp4 video | YouTube]
• Metabolomics Analysis Tools [brief tour (3:26) mp4 video | YouTube] [detailed tutorial (24:09) mp4 video | YouTube]
• Omics Dashboard Part 1 (16:35) [mp4 video], or [YouTube]
• Omics Dashboard Part 2 (24:29) [mp4 video], or [YouTube]

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.

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

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:

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

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.

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