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MetaCyc Metabolic Pathway Database
MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life.
MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
MetaCyc currently contains 3,105 pathways, 18,566 reactions and 18,973 metabolites.
MetaCyc applications include:
- Online encyclopedia of metabolism
- Predict metabolic pathways in sequenced genomes
- Support metabolic engineering via enzyme database
- Metabolite database aids metabolomics research
Tutorial #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]
Tutorial #2: Introduction to SmartTables
The following tutorial will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The tutorial 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]
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This tutorial 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]
Tutorial #4: Omics Data Analysis
This tutorial 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]
Tutorial #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]
Tutorial #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) [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]
Tutorial #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 Tutorial (42:15): "Structured Advanced Query Page" [Windows Media Video] or [mp4 video] or [YouTube]