Campus Units

Electrical and Computer Engineering, Genetics, Development and Cell Biology, Virtual Reality Applications Center

Document Type

Book Chapter

Publication Version

Accepted Manuscript

Publication Date


Journal or Book Title

Medical Informatics

First Page


Last Page





Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and create due to the diverse types of information that need to be represented. This chapter describes a suite of interlinked tools for developing, displaying, and modeling metabolic networks. The metabolic network interactions database, MetNetDB, contains information on regulatory and metabolic interactions derived from a combination of web databases and input from biologists in their area of expertise. PathBinderA mines the biological “literaturome” by searching for new interactions or supporting evidence for existing interactions in metabolic networks. Sentences from abstracts are ranked in terms of the likelihood that an interaction is described and combined with evidence provided by other sentences. FCModeler, a publicly available software package, enables the biologist to visualize and model metabolic and regulatory network maps. FCModeler aids in the development and evaluation of hypotheses, and provides a modeling framework for assessing the large amounts of data captured by high-throughput gene expression experiments.


This is a manuscript of a chapter published as Dickerson, Julie A., Daniel Berleant, Pan Du, Jing Ding, Carol M. Foster, Ling Li, and Eve Syrkin Wurtele. "Creating, modeling, and visualizing metabolic networks." In Medical Informatics, pp. 491-518. Springer, Boston, MA, 2005. doi: 10.1007/0-387-25739-X_17. Posted with permission.

Copyright Owner

Springer Science+Business Media, Inc.



File Format


Published Version