Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.

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BioCyc Guided Tour

This page provides a tour of the different types of object displays available through BioCyc. Each of the different pages that follow displays a different type of object, using different software visualization procedures.

These pages can be generated through queries from the "Search" menu at the top of every BioCyc web page, and they can be generated by clicking from one page to another.

A convenient way to take the guided tour is to keep this page visible in one tab in your Web browser, while viewing the other pages listed in a separate browser tab.

  1. Begin the tour at:
  2. In the operon diagram at the bottom of the gene page, click on the promoter to display:
  3. Toward the bottom of the transcription-unit page, click on "TyrR-tyr" to display
  4. Back in the gene page for tyrB, click on its map position 91.927 to display
    • Genome browser focused on tyrB
  5. Back in the gene page for tyrB, click on the "Align in Multi-Genome Browser" button in the set of buttons mid-way down the page. Select a set of organisms in the next page and click Submit near the bottom of the page. The resulting page will align the tyrB gene across all the selected organisms, when present. Example:
    • Comparative genome browser focused on tyrB

  6. Back in the gene page for tyrB, click on the pathway name "leucine biosynthesis" to display
  7. Within that pathway display click on the arrow for the last reaction to display
  8. Click on the chemical structure of leucine in the reaction page to display

  9. Click on one of the transport reactions near the end of the leucine page to display
  10. Click on "leucine ABC transporter" to display

  11. From the "Tools" menu at the top of the page, click on "Cellular Overview" to display the Cellular Overview (metabolic map diagram) for E. coli. This diagram can be magnified using the ladder on the left.
  12. Click on Tools → Regulatory Overview  to display a regulatory network diagram for E. coli. This diagram can also be magnified.
  13. Tools → Omics Viewers  allow you to paint high throughput data (expression data, metabolomics data, etc.) on the preceding diagrams. For examples see sample data files and animations.

  14. Tools → Comparative Analysis  will allow you to compare genome and pathway information.

  15. Let's now look at information for another organism, Aquifex aeolicus. You can switch the current organism that BioCyc queries by:
    • Clicking on the blue "change" link in the upper-right corner of every page
    • Clicking on the "change" link at the bottom of the "Search" or "Tools" menu on the top of every page

  16. After switching the current organism to Aquifex aeolicus, click on Tools Menu → Reports →  Summary statistics to see how and when the database for this organism was created.
  17. Click on Tools Menu → Reports →  Pathway Evidence or Tools Menu → Reports →  Pathway Holes to see summaries of all predicted pathways in this organism, and of the missing enzymes from those predicted pathways.

    Click the box next to "Pathways" to generate a comparison of their pathways, then click the boxes next to the names of these two organisms, and then click Submit at the bottom of the page to see this report. Like to learn more? Read the Guide to BioCyc or watch BioCyc Web seminars.