title: Presenting and exploring biological pathways with PathVisio.
abstract: BACKGROUND
  Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects. The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs.
  
  
  RESULTS
  PathVisio can be combined with other bioinformatics tools to open up three possible uses: visual compilation of biological knowledge, interpretation of high-throughput expression datasets, and computational augmentation of pathways with interaction information. PathVisio is open source software and available at http://www.pathvisio.org.
  
  
  CONCLUSIONS
  PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.
authors.affiliation: Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands. martijn.vaniersel@bigcat.unimaas.nl
authors.forename: Martijn P
authors.initials: MP
authors.lastname: van Iersel
authors.forename: Thomas
authors.initials: T
authors.lastname: Kelder
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.forename: Susan
authors.initials: S
authors.lastname: Coort
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Conklin
authors.forename: Chris
authors.initials: C
authors.lastname: Evelo
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome