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    A cropped version of the image Chandra by Dinesh Valke. Used under creative commons license.

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    Polar bear in water

    Polar bear by Leszek.Leszczynski. Used under creative commons license.

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

Guide To MetaCyc

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Learning Library

Tutorial Series

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.
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.
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.
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.
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.
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.
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.