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Presenting and exploring biological pathways with PathVisio

Martijn P van Iersel1 email, Thomas Kelder1 email, Alexander R Pico2,3 email, Kristina Hanspers2,3 email, Susan Coort1 email, Bruce R Conklin2,3 email and Chris Evelo1 email

Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands

Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA

Departments of Medicine, and Molecular and Cellular Pharmacology, University of California, San Francisco, CA 94158, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:399doi:10.1186/1471-2105-9-399

Published: 25 September 2008

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 webcite.

Conclusion

PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.


© 1999-2009 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.