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MetaCyc
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  • 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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    Rauvolfia serpentina

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

  • Vitamin D

    It is well known that vitamin D is produced in our skin during exposure to the sun. But did you know it is made from cholesterol?

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    Vitamin D

    Paradise waiting by .craig. Used under creative commons license.

  • DMSP Degradation

    Biological processes influence geochemical cycles. The main input of sulfur to the atmosphere is dimethyl sulfide, which is formed by microbial degradation of marine algae biomass.

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    Sulfur

    Mount sulfur by akahawkeyefan. Used under creative commons license.

  • So what killed this guy?

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    So what killed this guy?

    Napoleon at Sainte-Helene by Francois Joseph Sandmann. Public domain.

  • Twenty people were executed around Salem, MA for using witchcraft to afflict young girls. Were the victims bewitched, or could it be something they ate?

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    Maxinne Sentinna by Dame Gothel

    Maxinne Sentinna by Dame Gothel. Used under creative commons license.

  • Have you ever swum in the ocean and started to itch? Care to know why?

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    Coral Reef by Susan Hazlett, USGS

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

  • Beer is the world's most widely consumed alcoholic drink, and, with evidence dating as far back as 5000 BCE, one of its oldest. Did the ancient Egyptians know all about bitter acids?

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    Field

    Breja by Daniel Filho. Used under creative common license

  • We all know about the A, B, and O blood types, but did you know that a single glycosyltransferase is responsible for all of this diversity?

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    Field

    Blood Cells by Andrew Mason. Used under creative common license

  • 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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    Field

    Empty? by Arkadiusz R. Used under creative common license

  • When oil companies started adding MTBE to gasoline, it seemed like a good idea. Now it is banned in the US, and it is up to the bacteria to degrade the remaining contamination.

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    Field

    Hanoi Traffic at traffic lights by HoangP Used under creative common license

MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2937 pathways from 3295 different organisms.

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 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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Learning Library

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.