Skip to main content

Browsing Metabolic and Regulatory Networks with BioCyc

  • Protocol
  • First Online:
Bacterial Molecular Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))


The BioCyc database collection at integrates genome and cellular network information for more than 1,100 organisms. This method chapter describes Web-based tools for browsing metabolic and regulatory networks within BioCyc. These tools allow visualization of complete metabolic and regulatory networks, and allow the user to zoom-in on regions of the network of interest. The user can find objects of interest such as genes and metabolites within the networks, and can selectively examine the connectivity of the network. The EcoCyc database within the BioCyc collection has been extensively curated. The descriptions within EcoCyc of the Escherichia coli metabolic network and regulatory network were derived from thousands of publications. Other BioCyc databases received moderate levels of curation, or no curation at all. Those databases receiving no curation contain metabolic networks that were computationally inferred from the annotated genome sequences of each organism.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others


  1. Caspi R, Altman T, Dale J, Dreher K, Fulcher C, Gilham F, Kaipa P, Karthikeyan A, Kothari A, Krummenacker M, Latendresse M, Mueller L, Paley S, Popescu L, Pujar A, Shearer A, Zhang P, Karp P. (2010) The Meta-Cyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res, 38. (Database Issue): D473–D479.

    Google Scholar 

  2. BioCyc Database Collection. [].

  3. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res, 13(11):2498–2504.

    Article  PubMed  CAS  Google Scholar 

  4. Karp P, Paley S, Krummenacker M, Latendresse M, Dale J, Lee T, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler I, Caspi R. (2009) Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief Bioinformn, 11(1):40–79.

    Google Scholar 

  5. Keseler I, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus R, Johnson DA, Krummenacker M, Nolan L, Paley S, Paulsen I, Peralta-Gil M, Santos-Zavaleta A, Shearer A, Karp P. (2009) EcoCyc: A comprehensive view of E. coli biology. Nucleic Acids Res, 37:D464–D470.

    Google Scholar 

  6. BioCyc Webinars. [].

  7. BioCyc Downloads. [].

  8. Comparison of BioCyc Desktop Mode and Web Mode. [].

Download references


This work was supported by grant GM75742 from the National Institutes of Health. The contents of this chapter are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Mario Latendresse .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Latendresse, M., Paley, S., Karp, P.D. (2012). Browsing Metabolic and Regulatory Networks with BioCyc. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY.

Download citation

  • DOI:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics