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Introduction to BioCyc Genome and Metabolic Pathway Web Portal

The BioCyc web portal from SRI International contains integrated genome and metabolic-pathway databases for more than 20,000 sequenced organisms, including 60 curated databases. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation. BioCyc Pathway/Genome Databases (PGDBs) are organized into tiers according to the amount of manual updating they have received:

  • Tier 1 PGDBs received intensive manual curation efforts, and are updated frequently
  • Tier 2 PGDBs were computationally generated and have received moderate manual curation
  • Tier 3 PGDBs were computationally generated and have received no manual curation

For a list of available databases, click here.

PGDBs describe the genome of an organism, as well as its biochemical pathways; for a small fraction of organisms regulatory networks are also present. New releases occur three times per year, often including new databases as well as updated data. Two members of the BioCyc collection, the EcoCyc and MetaCyc databases, are derived from more than three decades of literature-based curation of genome and pathway data. Other members of the BioCyc database collection include HumanCyc and BsubCyc.

The Pathway Tools software combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of extensive PGDB data. For a full list of analysis and visualization tools please refer to the Pathway Tools Data Sheet or view the BioCyc overview video.

BioCyc Features

Pathway/Genome Web Portal for 20,000 Organisms

BioCyc has 20,000 databases including 60 plus curated databases. For a listing of databases, click here.

Each BioCyc PGDB describes the genome of an organism, as well as its biochemical pathways and, for a small fraction of organisms, its regulatory network.

Manually Curated Databases

  • EcoCyc: The data in this Escherichia coli K-12 MG1655 database have been gathered during two decades of literature-based curation from more than 40,000 articles. EcoCyc describes the metabolic, transport, and regulatory machinery of E. coli. EcoCyc curators have authored the equivalent of 3,600 textbook-pages of mini-review summaries for E. coli genes and pathways.
  • MetaCyc: Contains 3,006 metabolic pathways and 17,800 biochemical reactions from all domains of life. MetaCyc data and commentary were gathered from 71,000 publications to provide a comprehensive metabolic encyclopedia whose mini-review summaries encompass the equivalent of 10,079 textbook pages.

Computationally Generated Databases with some Manual Curation

  • YeastCyc: This highly curated metabolic network for Saccharomyces cerevisiae was curated from 47,000 publications.
  • HumanCyc: This database was derived from a computational pathway analysis of the human genome, followed by literature-based curation of human pathways and enzymes.
  • BsubCyc: The curated metabolic and regulatory networks for this Bacillus subtilis database cite 7,000 publications. Included are 180 regulatory genes controlling 1,200 regulated genes.
  • Mycobacterium tuberculosis, Corynebacterium glutamicum, Peptoclostridium difficile, Bacillus anthracis, Francisella tularensis, Helicobacter pylori, Vibrio cholerae, and others.

Computationally Generated Databases

Eukaryotic databases in BioCyc include Rattus norvegicus, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana.

All PGDBs include the genome, predicted metabolic pathways, and predicted pathway hole fillers (genes coding for missing enzymes in metabolic pathways). Bacterial PGDBs include predicted operons. The exact types of data present in different databases will vary. Many databases also include:

  • Protein subcellular locations, enzyme kinetics data, protein features, Gene Ontology terms, predicted Pfam domains
  • Curated regulatory information including promoters, operons, transcription-factor binding sites
  • Reaction atom mappings (map atoms from reactants to products)
  • Ortholog relationships to other BioCyc genomes, organism phenotypes
  • Database links

For an overview of BioCyc, visit http://bioinformatics.ai.sri.com/ptools/webinars/2020webinars/2020INTROBIOCYC01.mp4

A sample of the most popular BioCyc informatics tools:

  • Comprehensive search options (Genes, Proteins, RNAs, Compounds, Reactions, Pathways, Articles and more)
  • Omics Data Analysis
  • Genome Browser
  • Metabolic-map and regulatory-network viewers
  • Run Metabolic Model
  • Metabolic route search
  • BLAST and sequence pattern searches
  • Browse Pathway Ontology
  • Comparative Analysis
  • SmartTables

Curated Genome and Metabolic Pathway Data Derived from 130,000 Publications

BioCyc curators summarize and synthesize information from thousands of publications, saving scientists time in literature research, and integrating data for large-scale computational analyses.

BioCyc flow figure

BioCyc data include:

  • Genomes
  • Gene essentiality data
  • Regulatory networks
  • Gene Ontology terms
  • Orthologs
  • Protein features (e.g., enzyme active sites)
  • Protein functions
  • Metabolic pathways
  • Metabolites
  • Growth media and growth observations

Extensive Genome Informatics and Comparative Genomics Tools

BioCyc provides a powerful and comprehensive set of features for querying, visualization, and analysis of BioCyc data and user data. Some of our more popular tools are listed here.

Genome Browser Image

Genome Browser

Genome browser depiction of a region of the E. coli chromosome.

Gene colors indicate operon organization. Promoters and terminators are depicted when known. Pseudogenes are marked with X’s.

Comparative Genome Browser Image

Comparative Genome Browser

Aligns genome regions around orthologous genes.

Regulatory Overview Image

Regulatory Network Viewer

The Regulatory Overview depicts the transcriptional regulatory network in a PGDB. Here, the E. coli regulatory network is highlighted to show genes that regulate the gntR gene (blue lines), and the genes that are regulated by gntR (purple lines). The inner two rings are populated by transcription factors and sigma factors; the outer ring contains other genes.

Omics data analysis tools

Omics Viewer

Cellular Omics Viewer

The BioCyc Cellular Omics Viewer enables the user to paint omics datasets onto organism-specific metabolic network diagrams . Scientists can interpret high-throughput datasets in a pathway context, including animation of time-course or comparative datasets. Reaction lines can be colored with gene expression, proteomics, or reaction flux data; compound nodes can be colored with metabolomics data. Multi-omics data can be analyzed by coloring data onto reactions and metabolites simultaneously. Omics pop-ups graph omics data values using bar graphs, heat maps, or X-Y plots.

Omics Dashboard

Omics Dashboard

The BioCyc Omics Dashboard enables the user to rapidly survey how all cellular systems are responding to a given stimulus. Scientists can quickly view the response of genes within one or more specific systems of interest, and can gauge the relative activity levels of different cellular systems. The Dashboard also enables comparison of expression levels of a cellular system with those of its known regulators. The Dashboard consists of a set of panels, each representing a system of cellular function. Each panel shows a graph depicting omics data for each of a set of subsystems. Multiple timepoints or experimental conditions are plotted as separate data series within the graphs. Clicking on a panel drills down into its component subsystems.

Advanced Database Access

  • Extensive query tools available under Tools > Search menu.
  • Extensive web services APIs provided.
  • Author advanced queries: The Structured Advanced Query Form enables intuitive construction of database queries of SQL power using a Web-based interface.

Purchase Subscription

A subscription is required to access BioCyc.

Does your institution already have access?

BioCyc Subscriptions for Academic/Non-Profit Institutions

An institutional subscription provides unlimited, unrestricted access to all of the 20,000 databases within the BioCyc.org web portal, as well as to downloadable versions of the BioCyc databases. A BioCyc subscription covers access for all faculty, staff, and students at your institution, also includes off-campus access through any proxy IP addresses.

Subscription Pricing

Annual or multiyear subscription prices are based on the prior year's level of BioCyc website usage (number of page views) by your institution. Price levels range from Level 6 (highest) to Level 1 (lowest). Please contact us for your institution's pricing classification and we will provide your prior year usage and a quote for the current year. An academic consortium discount is available, if two or more institutions subscribe together with the same or identical license agreements – please contact us for more information.

Note: Development of MetaCyc and EcoCyc are currently supported by grants and do not require a subscription for access. Accordingly, your institution's MetaCyc and EcoCyc usage will be subtracted from your total BioCyc usage when calculating your pricing level.

Pricing Level Non-Profit/Academic 2022 (USD)
Level 6 $10,733
Level 5 $7,906
Level 4 $5,644
Level 3 $3,947
Level 2 $2,590
Level 1 $1,346

Multi-Year Pricing

Multi-year subscriptions provide overall price stability and eliminate renewal time and effort each year. We have two types of multi-year subscriptions: Paid Annually and Prepaid. We have 2 or 3-year options available.

Paid Annually: Paid Annually subscriptions cap your price increase for future years. With this option, you would pay each year's amount at the beginning of the subscription period, with a set 3% increase per year.

Prepaid: Prepaid subscriptions keep your fee locked in for future years. Pay the full amount for all years at the beginning of the subscription period, with no increase in price from this year's pricing.

We support EZ-Proxy

Many of our subscribers use EZ-Proxy for their off-campus access.

If you are a subscriber and need our configuration stanza, it is as follows:

Title BioCyc
URL https://biocyc.org
H https://www.biocyc.org/
H https://ecocyc.org/
H https://www.ecocyc.org/
H https://metacyc.org/
H https://www.metacyc.org/
H https://humancyc.org/
H https://www.humancyc.org/
H https://bsubcyc.org/
H https://www.bsubcyc.org/
H http://brg-files.ai.sri.com
DJ biocyc.org
DJ ecocyc.org
DJ metacyc.org
DJ humancyc.org
DJ bsubcyc.org
DJ brg-files.ai.sri.com

BioCyc Subscriptions for Commercial Institutions

A company-wide subscription provides unlimited, unrestricted access to all of the 20,000 databases within BioCyc for all employees at your company. A subscription also includes remote access through any proxy IP addresses.

Commercial Subscription Pricing

Annual or multiyear subscription prices are based on the prior year's level of BioCyc website usage (number of visits) by your company. Price levels range from Level 6 (highest) to Level 1 (lowest). Please contact us for your company's pricing classification and we will provide your prior year usage and a quote for the current year.

Note: MetaCyc and EcoCyc are currently supported by grants and do not require a subscription. Accordingly, your company's MetaCyc and EcoCyc usage will be subtracted from your total BioCyc usage when calculating your pricing level.

Pricing Level For-Profit/Corporate 2022 (USD)
Level 6 $38,317
Level 5 $28,222
Level 4 $20,147
Level 3 $14,090
Level 2 $9,337
Level 1 $4,804

Individual Subscriptions

We highly recommend that you ask your library to purchase an institutional subscription before purchasing an individual subscription yourself. Institutional subscriptions are usually more cost-effective and in most cases, libraries are willing to pay for the subscription if there is a substantial need for the resource and if they have room in their journal budget.

However, if your library or company is not able to subscribe at the current time, we do provide the option to subscribe at the individual level.

Each individual user (including multiple individuals in the same lab) will need their own subscription. Access will be granted via your existing BioCyc account.

Academic/Non-Profit Individual Use Subscription Pricing

$275 (USD) per person, per year.

For-Profit/Company Individual Use Subscription Pricing

$1,130 (USD) per person, per year.


Contact us with purchase questions

Teaching Access

As part of our mission to foster and promote scientific knowledge, we actively support the use of BioCyc for teaching purposes. If you wish to use BioCyc as an instructional material and your institution has not subscribed, please fill out this Google form to request courtesy educational access for you and your students for the duration of your course.

It's just our way of saying thanks... we value teachers!

Sponsored by:

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FAQ

I only use MetaCyc or EcoCyc. Will I need a subscription for access?

No, you do not currently need a subscription to access these databases.


I am having trouble getting BioCyc to recognize my subscription

Please see our Troubleshooting page.


Can I just get a subscription to one database within BioCyc for a lower price?

No, all subscriptions provide the same level of access: unrestricted access to all databases within BioCyc.


My institution or company has a subscription to BioCyc, but I am being prompted to log in to access the database. What should I do?

After a small number of free access, all BioCyc users are asked to create free accounts, even if their institution subscribes.

In addition, if you are off-campus, make sure you are accessing BioCyc through your library's or company's VPN or proxy server. If you don't know how to do this, please contact your librarian or IT department. If you are on-campus, please contact us with a screenshot of the issue and your public IP address where you are experiencing the issue.


What will happen if my institution/company/I don't have a subscription?

You can obtain a free trial for BioCyc for one-month by creating a BioCyc account. Once the one month has expired, you will only be able to access the free databases EcoCyc and MetaCyc.


My library's fiscal year is closed so we will need to wait to purchase new materials. Can we get access now?

Please contact us to discuss your options.


I am a faculty member at an institution. How can I set up subscription access for my institution?

The best way to do this is by contacting your librarian to request a subscription. If you can't find your librarian's contact information, please contact us and we can try to help you locate this information.


I use BioCyc at a nonprofit institution, but I am not a faculty member. What can I do to help set up a subscription for my institution?

The best way to do this is also by contacting your librarian (as mentioned in the last question), but your request will be more effective if you ask your lab head or Principal Investigator (i.e., a faculty member) to submit the request to your library.


My company has strict data security policies, or it only allows us to access data through our own internal software. Is there a way we can download your data to keep in-house?

Yes, please contact us about your unique situation -- it is possible to create an internal mirror for BioCyc.