title: CytoGEDEVO-global alignment of biological networks with Cytoscape.
abstract: In the systems biology era, high-throughput omics technologies have enabled the unraveling of the interplay of some biological entities on a large scale (e.g. genes, proteins, metabolites or RNAs). Huge biological networks have emerged, where nodes correspond to these entities and edges between them model their relations. Protein-protein interaction networks, for instance, show the physical interactions of proteins in an organism. The comparison of such networks promises additional insights into protein and cell function as well as knowledge-transfer across species. Several computational approaches have been developed previously to solve the network alignment (NA) problem, but only a few concentrate on the usability of the implemented tools for the evaluation of protein-protein interactions by the end users (biologists and medical researchers).
  
  
  
  We have created CytoGEDEVO, a Cytoscape app for visual and user-assisted NA. It extends the previous GEDEVO methodology for global pairwise NAs with new graphical and functional features. Our main focus was on the usability, even by non-programmers and the interpretability of the NA results with Cytoscape.
  
  
  
  CytoGEDEVO is publicly available from the Cytoscape app store at http://apps.cytoscape.org/apps/cytogedevo In addition, we provide stand-alone command line executables, source code, documentation and step-by-step user instructions at http://cytogedevo.compbio.sdu.dk
  
  
  
  malek@tugraz.at
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Saarland University, 66123 Saarbrücken, Germany Institute for Knowledge Discovery, Graz University of Technology, 8010 Graz, Austria.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Malek
authors.affiliation: Saarland University, 66123 Saarbrücken, Germany Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
authors.forename: Rashid
authors.initials: R
authors.lastname: Ibragimov
authors.affiliation: Institute for Knowledge Discovery, Graz University of Technology, 8010 Graz, Austria BioTechMed-Graz, Graz, Austria.
authors.forename: Mario
authors.initials: M
authors.lastname: Albrecht
authors.affiliation: University of Southern Denmark, Odense, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
mesh_terms: D019295:Computational Biology / Q000379:methods*; D011381:Programming Languages; D060066:Protein Interaction Maps; D011506:Proteins; D012984:Software; D049490:Systems Biology
chemical_list: D011506:Proteins