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MetaCyc
Metabolic Encyclopedia

Extensive, Highly Curated Data

BioCyc integrates genome data with a comprehensive body of additional data including metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings.

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[画像:Portion of Genome Browser]

Genome Browser image

A Vast Set of Bioinformatics Tools

Browsers for genomes, metabolic networks, and regulatory networks. Transcriptomics and metabolomics data analysis, comparative analysis, and metabolic route search. Sequence search and alignment.

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BioCyc for Synthetic Biology

Curated Pathway/Genome Databases for key chassis organisms

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Fuel Your Research

Kickstart your research with BioCyc mugs. Our Cyc-branded mugs are perfect for late-night analysis sessions or early mornings at your desk. Stylish, dishwasher-safe, and designed for the scientifically inclined. Get Cyc'd for your daily dose of caffeine!

Purchase BioCyc mugs

 

Explore Metabolic Maps for Thousands of Organisms

The Cellular Overview enables you to browse through zoomable metabolic map diagrams that are customized to each BioCyc organism.

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[画像:a portion of a Cellular Overview diagram, showing several pathway classes]

Cellular Overview image generated by Pathway Tools.

Metabolic Reconstruction from Sequenced Genomes

Install SRI's Pathway Tools software (free to academics) to predict metabolic pathways for sequenced genomes, generate metabolic models.

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Gene Expression Data Analysis

Multiple tools are available in this website for analysis of gene expression data.

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Comparative Genome Analysis

Multiple comparative analysis tools are available in this website.

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The BioCyc Database Collection

Tier 1 databases such as EcoCyc are the most highly curated. BioCyc databases are computationally derived from MetaCyc.

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Request Addition of New Genome to BioCyc

The Omics Dashboard: A New View of Omics Data

Visualize omics data as a set of graphs hierarchically organized by functional category. Drill down for more detail in areas of interest.

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20,080 Pathway/Genome Databases to Search

BioCyc is a collection of 20,080 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 153,000 publications, and is produced through an international collaboration.

The EcoCyc and Faecalibacterium prausnitzii A2-165 databases are freely available. Access to the other 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.

What people are saying
See more BioCyc testimonials

"BsubCyc is a tool of the utmost value."

Penn State

Paul Babitzke
Prof. of Biochemistry
& Molecular Biology

"My lab uses these resources on a daily basis."

University of Wisconsin

Patricia Kiley,
Professor and Chair,
Dep't. of Biomolecular Chemistry

"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."

University of Minnesota

Arkady Khodursky
Assoc. Prof. Biochemistry

"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."

Pacific Northwest National Lab

William Cannon, Team Lead
Computational Biology

"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."

Ginkgo Bioworks

"BioCyc is a tremendous resource for pathway analysis in metabolomics."

University of Georgia

Art Edison, Dept of Genetics

"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."

Great Lakes Bioenergy

Timothy J. Donohue, Director

"I have not found another database that has a better interface than BioCyc."

University of Michigan

Gary B. Huffnagle, Professor
Microbiology and Immunology

Learning Library

Tutorial Videos

Tutorial #1: Introduction to BioCyc
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
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.