Is Flawed Data Compromising Your Research?

BioCyc curators correct several hundred annotation errors per genome in our Tier 1-2 databases, ensuring your publications and proposals stand on a solid foundation.

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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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Collage of screenshots of portions of 4 different BioCyc Tools. Upper left: the Regulatory Overview, with some connections shown. Upper right: the Cellular Overview with omics data overlaid. Lower left: the Omics Dashboard. Lower right: the Comparative Genome Browser.

 

BioCyc for Synthetic Biology

Curated Pathway/Genome Databases for key chassis organisms enable trustworthy engineering of cellular networks.

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synbio

 

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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a portion of a Cellular Overview diagram, showing several pathway classes

Cellular Overview image generated by Pathway Tools.

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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a schematic showing 3 hypothetical routes from one compound to another, one that is very long, one that is short but most of the atoms from the starting compound do not end up in the target compound, and the best route, which is intermediate in length but conserves the atoms in the starting compound.

 

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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Two men looking at two screens, one showing a genome browser display, the other a regulatory overview display. Behind the screens is a blue background with a portion of a cellular overview diagram visible.

 

Gene Expression Data Analysis

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

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a portion of a cellular overview diagram, overlaid with a gene expression time series dataset. Detail popups are shown for three reactions in three different styles: a bar chart, a heatmap, and a line graph.

Cellular Overview Omics Viewer image generated by Pathway Tools.

Comparative Genome Analysis

Multiple comparative analysis tools are available in this website including aligning genomes at orthologous genes.

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A fragment of a Comparative Genome Browser display showing the region around the trpA gene for 5 E. coli strains. Orthologous genes are colored the same color in each strain.

Multi-organism Genome Browser image generated by Pathway Tools.

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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A portion of an Omics Dashboard display, showing panels for Biosynthesis and Degradation, and a popup showing details for L-alanine biosynthesis.

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...

"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

See more BioCyc testimonials

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.
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.