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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Portion of Genome Browser

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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Collage of BioCyc Tools

 

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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Cellular Overview

Cellular Overview image generated by Pathway Tools.

Shigella flexneri on your iPhone and iPad

Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse BioCyc on the go! Try the iPad version as well.

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BioCyc iOS App for iPhone/iPad

BioCyc iOS App for iPhone/iPad

RouteSearch: Search for Paths Through the Metabolic Network

Search for lowest-cost paths through the metabolic network of the selected organism.

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Route Search Diagram

 

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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Locally Installed Omics Viewer Image

 

Gene Expression Data Analysis

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

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WebOmics Image

Cellular Overview Omics Viewer image generated by Pathway Tools.

Comparative Genome Analysis

Multiple comparative analysis tools are available in this website.

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Multi-Genome Browser

Multi-organism Genome Browser image generated by Pathway Tools.

Search Databases by Organism Properties

BioCyc contains data on phenotypic properties of organisms, such as human-microbiome body site, aerobicity, and temperature range.

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Illustration of several bacteria

Image by Arek Socha from Pixabay

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
Diagram of three tiers of Databases within BioCyc

BioCyc Database Collection

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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Dashboard Image

Cellular Dashboard image generated by Pathway Tools.

Shigella flexneri Pathway/Genome Databases

This website contains 38 Shigella flexneri genomes (show list) and associated metabolic pathways. This site is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click on the "Change Current Database" button (above) to explore the available databases.

This site includes extensive retrieval, visualization and analysis tools, including a genome browser and a metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Shigella flexneri and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.

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.