title: Metabolic network visualization eliminating node redundance and preserving metabolic pathways.
abstract: BACKGROUND
  The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.
  
  
  RESULTS
  We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.
  
  
  CONCLUSIONS
  The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.
authors.affiliation: LaBRI, Université Bordeaux I, 351 Cours de la libération, 33405 Talence CEDEX, France. bourqui@labri.fr
authors.forename: Romain
authors.initials: R
authors.lastname: Bourqui
authors.forename: Ludovic
authors.initials: L
authors.lastname: Cottret
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacroix
authors.forename: David
authors.initials: D
authors.lastname: Auber
authors.forename: Patrick
authors.initials: P
authors.lastname: Mary
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
authors.forename: Fabien
authors.initials: F
authors.lastname: Jourdan
mesh_terms: D000465:Algorithms; D000818:Animals; D002952:Citric Acid Cycle; D003196:Computer Graphics; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D016678:Genome; D053858:Metabolic Networks and Pathways / Q000235:genetics; D051379:Mice; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014633:Valine / Q000096:biosynthesis
chemical_list: D014633:Valine