Information Density: MetaCyc – Signal Evidence & AI Readability

[IMG: MetaCyc]

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[H3] Ajmaline is an antiarrhythmic agent produced by the plant Rauvolfia serpentina. Why is it named after the Indian physician Hakim Ajmal Khan?

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[IMG: Rauvolfia serpentina, a plant with red stems and blue-black berries]

A cropped version of the image Chandra by Dinesh Valke. Used under creative commons license.

[H3] Can the enzyme oxalate oxidase (EC 1.2.3.4) save the American chestnut? Yes, if you ask Darling 58.

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[IMG: Green spiky chestnut pods grow on a chestnut tree]

Chestnuts by Peter Burka. Used under creative commons license.

[H3] Saffron is arguably the most expensive spice in the world. But what does it have to do with Covid-19?

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[IMG: Purple saffron flowers]

Autumn crocus! by Sylvia Sassen. Used under creative commons license.

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[H3] The Bible tells us that the ancient Israelites were fed manna that fell from the sky while crossing the Sinai desert. But what is manna?

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[IMG: black and white photo of people walking in the Sinai desert]

Exodus by Giorgio Raffaelli. Used under creative commons license.

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[H3] Why did Cleopatra, the queen of Egypt, dilate her pupils to look larger? Well, we can't tell you why, but we can tell you how.

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[IMG: Cleopatra holding black cat Bastet]

Granted Audience with Cleopatra and Bastet by Stella Splendid. Used under Creative Commons license.

[H3]
Have you ever swum in the ocean and started to itch? Care to know why?

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[IMG: Man lying on surfboard in the ocean]

Coral
Reef, taken by Susan Hazlett, USGS. Public domain.

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[H3] How long can mammals live without oxygen? Find out!

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[IMG: Whimsical drawing of a naked mole rat]

IMG_20161015_161456 by Julie Freeman. Used under Creative Commons license

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[H3] Vanillin goes with desserts. Chilli peppers go with salsa. But you can't have salsa without vanillin.

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[IMG: row of chili peppers]

Chili pepper by hepp. Used under creative commons license

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[H3] Chitin is the second most common polymer in the world, after cellulose. Our understanding of its degradation was significantly boosted with the discovery of LPMOs. And what are LPMOs?

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[IMG: Irridescent blue beetle on a twig]

Empty? by Arkadiusz R. Used under creative common license

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[H3] What do bile acids have to do with a bear? And why you should be aware?

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[IMG: Polar bear in water]

Polar bear by Leszek.Leszczynski. Used under creative commons license.

[H1] MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic
pathways from all domains of life.
MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
MetaCyc currently contains 3,284 pathways, 20,199 reactions, and 20,642
metabolites.
MetaCyc applications include:

Online encyclopedia of metabolism
Predict metabolic pathways in sequenced genomes
Support metabolic engineering via enzyme database
Metabolite database aids metabolomics research

Guide To MetaCyc

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Request Free Classroom Use

[H2] What people are saying...

"BsubCyc is a tool of the utmost value."
[IMG: Penn State]
Paul BabitzkeProf. of Biochemistry& Molecular Biology

"My lab uses these resources on a daily basis."
[IMG: 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."
[IMG: University of Minnesota]
Arkady KhodurskyAssoc. Prof. Biochemistry

"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
[IMG: Pacific Northwest National Lab]
William Cannon, Team LeadComputational Biology

"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
[IMG: Ginkgo Bioworks]

"BioCyc is a tremendous resource for pathway analysis in metabolomics."
[IMG: University of Georgia]
Art Edison, Dept of Genetics

"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
[IMG: Great Lakes Bioenergy]
Timothy J. Donohue, Director

"I have not found another database that has a better interface than BioCyc."
[IMG: University of Michigan]
Gary B. Huffnagle, ProfessorMicrobiology and Immunology
See more BioCyc testimonials

[H2] Learning Library

[H3] Tutorial Videos

Tutorial #1: Introduction to BioCyc

Quick Introduction to BioCyc (4:30)
Searching in BioCyc (17:00)
Genes (15:00)
Genome Browser (11:45)
Pathways (13:19)
Reactions (3:37)
Compounds (6:42)

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.
SmartTables Overview (4:30)
SmartTables Basics (12:43)
SmartTables Transformations (8:08)
SmartTables Import and Export (9:00)
SmartTables Gene Expression Analysis (7:40)
Metabolomics Analysis with SmartTables (6:45)

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.
The Cellular Overview: Navigating metabolic networks (17:15)
Comparative Genomics (21:06)
Ortholog Viewing (10:02)
The Regulatory Overview -- exploring transcriptional regulatory networks (15:21)

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.
Transcriptomics Analysis Tools [brief tour (2:40)
Metabolomics Analysis Tools (3:26) [click here for a detailed tutorial]
Omics Dashboard (16:35)
Omics Dashboard Part (24:29)

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.
Pathway Collages (22:39)

Tutorial #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.
Part 1A: Introduction to Database Building and Pathologic (14:04)
Part 1B: Building a Database: Detailed Pathologic Example (23:53)
Part 2A: General Editing Strategies (8:00)
Part 2B: Creating and Editing Reactions and Compounds (17:32)
Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10)
Part 2D: Making and Editing Pathways (9:42)

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.
Structured Advanced Query Page Quick Introduction (6:27)
Structured Advanced Query Page Full Tutorial (42:15)

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Page generated by Pathway Tools version 29.5 (software by SRI International) on Sun May 24, 2026, BIOCYC16.EcoCyc version 29.6.

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Page generated by Pathway Tools version 29.5 (software by SRI International) on Sun May 24, 2026, BIOCYC16.EcoCyc version 29.6.