19494 Pathway/Genome Databases to Search
BioCyc is a collection of 19494 Pathway/Genome Databases (PGDBs) for model eukaryotes and for thousands of microbes, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 130,000 publications.
The EcoCyc and MetaCyc databases are freely available, but access to the remaining BioCyc databases requires a paid subscription.
The following websites are part of BioCyc. Opening these sites in your browser is a convenient way to pre-select that database for searches.
Webinar Series
Webinar #1: Introduction to BioCyc
These 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 (7:44) [mp4 video] or [YouTube]
- BioCyc Overview Part 2 (4:44) [mp4 video] or [YouTube]
- Searching in BioCyc (17:00) [mp4 video] or [YouTube]
- Genome Browsing, Searching, and Alignment (15:38) [mp4 video] or [YouTube]
- Pathways (13:19) [mp4 video] or [YouTube]
- Reactions (3:37) [mp4 video] or [YouTube]
- Compounds (6:42) [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]
- Part 3: SmartTables Transformations (8:08) [QuickTime Video]
- Part 4: SmartTables Import and Export (9:00) [QuickTime Video]
- Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video]
- Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video]
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 or YouTube] [detailed tutorial (21:36) mp4 video or YouTube]
- Metabolomics Analysis Tools [brief tour (3:26) mp4 video or YouTube] [detailed tutorial (24:09) mp4 video or 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
by, for example, overlaying omics data, altering the relative
positions of pathways, and modifying connections among pathways.
Learn 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
Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB)
for an organism with a sequenced and annotated
genome. Build a PGDB for your own lab or for the whole scientific community.
- 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) Clean Freshwater OEM 2004-2007 Evinrude 40/50/60 HP E-Tec Outboa 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
An introduction to the Structured Advanced Query Page, which allows
complex queries and queries across one or more databases in the
BioCyc collection. 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.
- 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]
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