VISIBIOweb : a web-based visualization and layout service for biological pathways
Author(s)
Advisor
Doğrusöz, UğurDate
2009Publisher
Bilkent University
Language
English
Type
ThesisItem Usage Stats
173
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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.