VISIBIOweb : a web-based visualization and layout service for biological pathways

Abstract

A biological pathway is a representation of biological reactions between molecules in a living cell. At present, there are hundreds of Internet-accessible databases storing biological pathway data. Exchanging, handling, and storing this data are crucial in terms of both providing understandability and allowing further enhancements on the gathered data. As a result of this necessity, many biological models were developed to cluster the data in a meaningful manner under a semantically reasonable hierarchy. As the amount and complexity of the data increases, visualization of pathways becomes inevitable. Graphs are inherently suitable for modeling pathways. The task of creating a visual representation for pathways dynamically requires methods from the area of graph visualization. As a result, many software systems, which can interpret the pathway data with a graph structure and visualize the constructed graph, emerged. However, many of these software systems are insufficient due to poor complexity handling of the underlying model, lack of visual standardization or long installation steps. In this thesis, we introduce VISIBIOweb, a new open-source and web-based visualization service for biological pathway models stored in BioPAX (Biological Pathways Exchange Language) format. VISIBIOweb runs on Apache Tomcat server and is implemented in Java based on Eclipse GEF (Graphical Editing Framework). Google Maps API is used on the client side as the core component to visualize the representation constructed on the server. VISIBIOweb supports basic graph viewing functionalities such as zooming, scrolling, and selection of graph objects. The inspector window is provided to view the properties of the selected graph object. Once the view for the uploaded biological model is created, it can be stored as a static image. The biological models can also be persisted and embedded within other web sites just like Google Maps. The layout information of the constructed graph is also provided in an XML-based format. The introduction of such a format is a good starting point to develop an official layout extension for BioPAX format.