Karp, P. D. (2009). The Multiple Scientific Disciplines Served by EcoCyc. In Systems Biology and Biotechnology of Escherichia coli (pp. 99-112). Springer, Dordrecht.
Abstract
The EcoCyc database integrates information about the E. coli genome, its metabolic pathways, and its regulatory network. EcoCyc is in use by scientists from a variety of disciplines. Experimental biologists use it as a reference source on E. coli, and to leverage information about E. coli to the study of other microbes. Because the E. coli genome has the largest number of experimentally characterized genes of any organism, EcoCyc is used in the annotation of other microbial genomes by sequence similarity. EcoCyc has also been used in a number of global biological studies by computational biologists, and to provide training and validation datasets for the development of new bioinformatics algorithms. EcoCyc serves as a reference source for metabolic engineers, and it is used in microbiology education. The software behind EcoCyc, called Pathway Tools, has been used to develop EcoCyc-like databases for many other organisms. Pathway Tools provides powerful query and visualization capabilities, including tools to analyze high-throughput datasets by painting those datasets onto genome-scale diagrams of the metabolic network, the transcriptional regulatory network, and the complete genome map.
Keywords
- Metabolic Network
- Discipline Serve
- Pathway Tool
- Metabolic Engineer
- Operon Prediction
