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OPERATIONS
LOGIN |  Why Login? |  Create New Account WHY CREATE AN ACCOUNT? An account provides several benefits. Through your account you can: * BioCyc accounts enable access to other sites such as EcoCyc andMetaCyc
* Create SmartTables of genes, metabolites, etc, and, optionally, associated datasets:* analyze them,
* store them,
* and share them with colleagues * Run and store metabolic models * Customize the appearance of pages * Store organism sets for comparative operations * Configure default settings for the Omics Viewers * Receive important email updates * Aid us in tracking site usage to ensure continued funding for thissite
* Participate in surveys about improvements for this websiteCreate New Account
Searching _  _ change organism database* Sites
* BioCyc
* EcoCyc
* MetaCyc
* HumanCyc
* BsubCyc
* Pathway Tools
* Search
* Search Genes, Proteins or RNAs* Search Compounds
* Search Reactions
* Search Pathways
* Search DNA or mRNA Sites * Search Growth Media * Search Full-text Articles* Advanced Search
* Cross Organism Search* BLAST Search
* BLAST All BioCyc
* Sequence Pattern Search * Google Search of this Site* Genome
* Genome Browser
* Genome Overview
* Regulatory Overview * Browse Gene Ontology * Map Sequence Coordinates * Generate Genome Poster* Metabolism
* Cellular Overview * Run Metabolic Model * Dead-end Metabolites * Chokepoint Reactions * Metabolic Route Search * Metabolite Translation Service* Pathway Collages
* Browse Pathway Ontology * Browse Enzyme Commission Ontology * Browse Compound Ontology * Generate Metabolic Map Poster* Analysis
* Comparative Analysis * Omics Data Analysis* Omics Dashboard
* Summary Statistics * Metabolomics Pathway Coverage * List Functional Gene Clusters * Update Notifications* Reports
* History of updates* Pathway evidence
* Pathway holes
* SmartTables
* Public SmartTables * Special SmartTables* Help
* Searching
* Website User Guide* Webinars
* Glossary
* PGDB Concepts Guide* Guide to BioCyc
* Contact Us/Licensing/Support BIOCYC DATABASE COLLECTION BioCyc is a collection of 14735 Pathway/Genome Databases (PGDBs), plus software tools for exploring them.
Key aspects of BioCyc data: * Quality data curated from tens of thousands of publications, including curated databases for _E. coli,_ _B. subtilis,_ _H. sapiens,_ and _S. cerevisiae._ * Computationally predicted metabolic pathways and operons. * Data integrated from other databases including gene essentiality, regulatory networks, protein features, and GO annotations. Current version: 23.1, released on Sept 19, 2019. Update History SUBSCRIPTIONS ARE REQUIRED TO ACCESS MOST OF BIOCYC BEYOND A LIMITED PERIOD OF FREE USE. For more information on obtaining a subscription,click here
.
Subscriptions support curation of BioCyc content on a non-profit basis. You do not need a subscription to access EcoCyc or MetaCyc, or if your institution already subscribes (institution name is in the top right corner of this page, or appearshere
.)
NEW TO BIOCYC? Typical usage is: * Select a database (genome) to search by clicking "change organism database" in the box in the top right of every page. * Search for a gene, pathway, metabolite, or enzyme using the Quick Search in that same box, or see the Search menu for more options.New User Guide >>
*
Cellular Overview image generated by Pathway 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.Learn More
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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. OR, DESIGN LOWEST-COST PATHWAYS TO NOVEL COMPOUNDS BY ADDING REACTIONS FROM METACYC.Learn More
*
METABOLIC RECONSTRUCTION FROM SEQUENCED GENOMES INSTALL SRI'S PATHWAY TOOLS SOFTWARE (FREE TO ACADEMICS) TO PREDICT METABOLIC PATHWAYS FOR SEQUENCED GENOMES, GENERATE METABOLIC MODELS, AND ANALYZE OMICS DATA.Learn More
*
SmartTable display generated by Pathway Tools. METABOLOMICS DATA ANALYSIS MULTIPLE TOOLS ARE AVAILABLE IN THIS WEBSITE FOR METABOLOMICS DATAANALYSIS.
Learn More
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Cellular Overview Omics Viewer image generated by Pathway Tools. GENE EXPRESSION DATA ANALYSIS MULTIPLE TOOLS ARE AVAILABLE IN THIS WEBSITE FOR ANALYSIS OF GENEEXPRESSION DATA.
Learn More
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Multi-organism Genome Browser image generated by Pathway Tools. COMPARATIVE GENOME ANALYSIS MULTIPLE COMPARATIVE ANALYSIS TOOLS ARE AVAILABLE IN THIS WEBSITE.Learn More
*
Photo of Grand Prismatic Spring,Yellowstone by Frank Kovalchek . Human Microbiome graphic by NIH MedicalArts and Printing
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Photo of soil samples by Oregon Department of Transportation . Used under creative commons license.
SEARCH DATABASES BY ORGANISM PROPERTIES BIOCYC NOW CONTAINS DATA ON PHENOTYPIC PROPERTIES OF ORGANISMS, SUCH AS HUMAN-MICROBIOME BODY SITE, AEROBICITY AND GEOGRAPHIC SAMPLECOLLECTION SITE.
Learn More
*
BioCyc Database Collection THE BIOCYC DATABASE COLLECTION TIER 1 DATABASES SUCH AS ECOCYC ARE THE MOST HIGHLY CURATED. BIOCYC DATABASES ARE COMPUTATIONALLY DERIVED FROM METACYC.Learn More Request
Addition of New Genome to BioCyc*
RECEIVE NOTIFICATIONS OF NEW RESEARCH IN YOUR INTEREST AREA IDENTIFY SPECIFIC GENES OR PATHWAYS OF INTEREST TO YOUR WORK, AND LET BIOCYC NOTIFY YOU BY EMAIL WHEN NEW CURATED INFORMATION IS AVAILABLE.Learn More
*
Cellular Dashboard image generated by Pathway Tools. THE CELLULAR 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.Learn More
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BIOCYC TOOLS
BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:* Genome browser
* Display of individual metabolic pathways , and of full metabolic maps * Multiple omics data analysis methods for user-supplied omics and multi-omics datasets including the Omics Dashboard , painting onto pathway diagrams and metabolic maps, and tables of perturbed pathways * Store groups of genes, metabolites, etc. in your account as SmartTables ; share, analyze, transform those groups * Metabolic route searchtools
* Run metabolic models * Comparative analysis toolsBIOCYC DATABASES
The BioCyc databases are divided into three tiers, based on theirquality.
Tier 1 databases have received at least one person-year of literature-based curation, and are the most accurate. EcoCyc and MetaCyc have each received more than 20 person-years of curation. Tier 2 and Tier 3 databases contain computationally predicted metabolic pathways, predictions as to which genes code for missing enzymes in metabolic pathways, and predictedoperons.
FUNDING SOURCES
The development of BioCyc is funded by NIH grants GM080746, GM077678, and GM075742 from the NIH National Institute of General Medical Sciences, and by BioCyc subscription revenues.VIDEO TUTORIALS
The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website and the PathwayTools software.
The video to the left introduces BioCyc and covers: * BioCyc site contents, including EcoCyc, MetaCyc, and our extensivedatabase collection
* How BioCyc databases are created, and the types of informationthey contain
* BioCyc accounts
GENERAL INFORMATION
Intro to BioCyc
Publications
Update History
Contact Us
About Us
DATA AND SERVICES
Software/Data DownloadsWeb Services & APIs
Linking to BioCyc
Metabolic and Genome Posters Request New BioCyc GenomeCREDITS
How to Cite
Steering Committee
FOLLOW US
Pathway Tools Blog
Mailing List
©2019 SRI International, 333 Ravenswood Avenue, Menlo Park, CA94025-3493
SRI International is an independent, nonprofit corporation. Privacy policy    DisclaimerClose
SPECIFY LIST OF ORGANISM DATABASES SELECT ONE OR MORE DATABASES:* _By Name_
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Find in tree:
Find organisms whose property:Select Property
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has values does not have values has any value has no value Exact Match Substring Match = (approx.) < ≤ > ≥ Select ValuesAND OR
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has values does not have values has any value has no value Exact Match Substring Match = (approx.) < ≤ > ≥ Select ValuesAND OR
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has values does not have values has any value has no value Exact Match Substring Match = (approx.) < ≤ > ≥ Select ValuesAND OR
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has values does not have values has any value has no value Exact Match Substring Match = (approx.) < ≤ > ≥ Select ValuesAND OR
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has values does not have values has any value has no value Exact Match Substring Match = (approx.) < ≤ > ≥ Select Values Shift-click to select a range; Ctrl-click to select multiple non-contiguous organisms. Database lists are saved as SmartTables that you can edit from your MySmartTables page.
Log in and reload this page to access your saved database lists. Tier 1 and Tier 2 databases are displayed with orange and gray backgrounds, respectively.CURRENT SELECTION
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