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Bioinformatics Advance Access originally published online on November 25, 2004
Bioinformatics 2005 21(8):1596-1602; doi:10.1093/bioinformatics/bti153
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

VitaPad: visualization tools for the analysis of pathway data

Matthew Holford 1, Naixin Li 1, Prakash Nadkarni 2 and Hongyu Zhao 1,3,*

1Center for Statistical Genomics and Proteomics, Yale University New Haven, CT 06520, USA
2Center for Medical Informatics, Yale University New Haven, CT 06520, USA
3Division of Biostatistics, Yale University New Haven, CT 06520, USA

*To whom correspondence should be addressed.

Motivation: Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data.

Results: VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance.

Availability: http://bioinformatics.med.yale.edu

Contacts: matthew.holford{at}yale.edu; hongyu.zhao{at}yale.edu


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