Overview

VitaPad stands for Visualization Tools for the Analysis of Pathway Diagrams. Basically, it allows users to create and edit diagrams of pathways or other biological networks, map experimental to them and store them in XML or a relational database. It is a desktop application written in Java and was built using a variety of open-source tools.

The primary objectives of this project are:

• To use a 'metadata' driven design for optimum flexibility and extensibility
• To be a fully open-source pathway visualization solution that also defined open standards for XML and database storage
• To take advantage of state-of-the-art graphics and UI capabilities for appealing diagrams and maximum usability
• To use sophisticated graph layout algorithms to quickly make sense of complicated pathways

Capabilities

At present, VitaPad's functionality can be summarized as follows:

1. Creation of original pathway diagrams
2. Modification of previously created diagrams
3. Mapping of experimental data, specifically microarray data to an existing diagram
4. Automatic generation of pathway diagrams through a spring-embedded layout algorithm
5. Storage of generated diagrams in an XML format
6. Persistence of diagrams in a relational database