title: Integrated network reconstruction, visualization and analysis using YANAsquare.
abstract: BACKGROUND
  Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network.
  
  
  RESULTS
  YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as well as target and robustness tests). YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). As application examples we set-up and model the phospholipid network in the phagosome and genome-scale metabolic maps of S.aureus, S.epidermidis and S.saprophyticus as well as test their robustness against enzyme impairment.
  
  
  CONCLUSIONS
  YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.
authors.affiliation: Department of Bioinformatics, Biocenter Am Hubland, D-97074 University of Würzburg, Germany. roland.schwarz@biozentrum.uni-wuerzburg.de
authors.forename: Roland
authors.initials: R
authors.lastname: Schwarz
authors.forename: Chunguang
authors.initials: C
authors.lastname: Liang
authors.forename: Christoph
authors.initials: C
authors.lastname: Kaleta
authors.forename: Mark
authors.initials: M
authors.lastname: Kühnel
authors.forename: Eik
authors.initials: E
authors.lastname: Hoffmann
authors.forename: Sergei
authors.initials: S
authors.lastname: Kuznetsov
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Gareth
authors.initials: G
authors.lastname: Griffiths
authors.forename: Stefan
authors.initials: S
authors.lastname: Schuster
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000592:standards; D003198:Computer Simulation / Q000592:standards; D053858:Metabolic Networks and Pathways; D012984:Software / Q000592:standards; D013223:Statistics as Topic