Presenting and exploring biological pathways with PathVisio.
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.
van Iersel
Martijn P
MP
Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands. martijn.vaniersel@bigcat.unimaas.nl
Kelder
Thomas
T
Pico
Alexander R
AR
Hanspers
Kristina
K
Coort
Susan
S
Conklin
Bruce R
BR
Evelo
Chris
C
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
D020543:Proteome