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Presenting and exploring biological pathways with PathVisio

  • Author(s): van Iersel, MP
  • Kelder, T
  • Pico, AR
  • Hanspers, K
  • Coort, S
  • Conklin, BR
  • Evelo, C
  • et al.

Published Web Location

https://doi.org/10.1186/1471-2105-9-399
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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. Conclusion: PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals. © 2008 van Iersel et al; licensee BioMed Central Ltd.

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This item is under embargo until December 31, 2999.