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Bioinformatics Advance Access published online on November 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti153
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 6, 2004
Revised October 20, 2004
Accepted November 12, 2004

Article

VitaPad: visualization tools for the analysis of pathway data

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

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

* To whom correspondence should be addressed.
Matthew Holford, E-mail: matthew.holford{at}yale.edu


  Abstract

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; and (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance.

Availability: ftp://anonymous:vitaTest@130.132.8.83.


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