Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014

EcoCyc E. coli Database

EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

New to EcoCyc? Take the guided tour of the EcoCyc.org Web site, watch our free online instructional videos, or read our 2013 article: "EcoCyc: fusing model organism databases with systems biology"

EcoCyc User Guide >>
  • Cascade

    Crystal structure of E. coli Cascade. Image from the RCSB PDB (www.rcsb.org) of PDB ID 1VY8 (R.N. Jackson et al. (2014) Science 345:1473-9).

    Cascade to the Rescue!

    From protecting E. coli against phage infection to the promise of gene therapy: How does Cascade do it? Recent crystal structures of the enzyme are improving our understanding of this enzyme.

    Learn More
  • Metabolic Model for E. coli K-12

    A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available.

    Learn More
  • Bam complex

    Schematic diagram of the Bam complex, Fig. 1a in Kim et al.. Used under creative commons license.

    Maintaining the Outer Membrane

    The 5-subunit Bam complex is responsible for the assembly and insertion of beta-barrel proteins into the OM of E. coli. Although a full understanding of its function in beta-barrel folding remains elusive, recent work has yielded many insights into subunit interaction and activity.

  • SmartTable display generated by Pathway Tools.

    Metabolomics Data Analysis

    Multiple tools are available in this website for metabolomics data analysis.

    Learn More
  • E. coli, bacteria, cryo FIB-SEM, dotted with silver nanoparticles

    BioCyc iOS App for iPhone/iPad

    EcoCyc App is now BioCyc App

    Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse EcoCyc on the go! The NEW BioCyc app comes preloaded w/ EcoCyc.

    Download Here
  • Multi-Genome Browser

    Multi-organism Genome Browser image generated by Pathway Tools.

    Comparative Genome Analysis

    Multiple comparative analysis tools are available in this website.

    Learn More
  • Cellular Overview Omics Viewer image generated by Pathway Tools.

    Gene Expression Data Analysis

    Multiple tools are available in this website for analysis of gene expression data.

    Learn More

Tools

BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:

PortEco

  EcoCyc's sister site PortEco now hosts E. coli omics data and powerful analysis tools.

How to Cite EcoCyc

Please cite EcoCyc as Keseler et al. (2013), "EcoCyc: fusing model organism databases with systems biology", Nucleic Acids Research 41: D605-12.

Funding Sources

The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences.

Video Tutorials

The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website and the Pathway Tools software. A complete list of videos in additional download formats are available on the Video and Podcast page.

This video introduces the BioCyc.org site and the BioCyc collection of hundreds of Pathway/Genome Databases and covers:

  • BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
  • How to search, browse, and find what you need in the BioCyc collection
  • How we represent metabolism, transcription, and all their parts