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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 3,128 pathways, 18,819 reactions and 19,173 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
What people are saying
"BsubCyc is a tool of the utmost value."
Prof. of Biochemistry
& Molecular Biology
"My lab uses these resources on a daily basis."
Professor and Chair,
Dep't. of Biomolecular Chemistry
"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."
Assoc. Prof. Biochemistry
"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
William Cannon, Team Lead
"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
"BioCyc is a tremendous resource for pathway analysis in metabolomics."
Art Edison, Dept of Genetics
"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
Timothy J. Donohue, Director
"I have not found another database that has a better interface than BioCyc."
Gary B. Huffnagle, Professor
Microbiology and Immunology
Webinar #1: Introduction to BioCyc
- BioCyc Overview Part 1 (14:04) [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
- 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
- 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
- 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
Webinar #6: Creating a Pathway/Genome Database
- Part 1A: Introduction to Database Building and Pathologic (14:04) [MP4 Video] or [YouTube]
- Part 1B: Building a Database: Detailed Pathologic Example (23:53) [MP4 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]