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  Genome Browser
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  • 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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  • 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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  • Explore Metabolic Maps for Thousands of Organisms

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

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    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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    Cellular Dashboard image generated by Pathway Tools.

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19534 Pathway/Genome Databases to Search

BioCyc is a collection of 19534 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 130,000 publications.

The EcoCyc and MetaCyc databases are freely available, but access to the remaining 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.


Webinar Series

Webinar #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.
Webinar #2: Introduction to SmartTables
The following webinar will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The webinar 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.
Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This webinar 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.
Webinar #4: Omics Data Analysis
This webinar will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Webinar #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.
Webinar #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.
Webinar #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.