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[HTML][HTML] Presenting and exploring biological pathways with PathVisio

MP van Iersel, T Kelder, AR Pico, K Hanspers… - BMC …, 2008 - Springer
MP van Iersel, T Kelder, AR Pico, K Hanspers, S Coort, BR Conklin, C Evelo
BMC bioinformatics, 2008•Springer
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 …
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.
Springer
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