Representation and Visualization of Genetic Regulatory Networks

We present a new framework, Sonnet, for the interactive visualization of large, complex biological models that are represented as graphs. Sonnet provides a flexible representation framework and graphical user interface for filtering and layout, allowing users to rapidly visualize different aspects of a data set. Many previous approaches have required users to write customized software in order to achieve the same functionality. With Sonnet, once features of interest are identified, they can be captured as figures for offline presentation. We demonstrate the application of Sonnet to the visualization and manipulation of transcriptional regulatory networks in yeast. Sonnet is particularly well adapted to this application as native presentation of these networks yields dense and difficult to decipher results. Thesis Supervisor: David Gifford Title: Professor of Computer Science and Engineering Dacheng Zhao 2 Acknowledgements I would like to express my profound gratitude towards my advisor, Professor David Gifford, for his support, mentorship and guidance. Prof. Gifford's vision and wisdom are extraordinary, and his invaluable feedback kept me focused. I would also like to thank Georg Gerber, a graduate student in the laboratory of Prof. Gifford. Georg's work in computational biology was the original inspiration for the project. Moreover, Georg's advice during all stages of this project-design, implementation, and write-upwas incredibly helpful and had a tremendous impact on the project. I would also like to thank my parents, Li Chen and Wei Zhao, and my brother, Derek Zhao, for supporting and nurturing me my entire life. My parents fostered my curiosity and instilled in me a deep appreciation for science and learning. Last but not least, I would like to thank my fiancee, Bonny Lee, for her immeasurable support. Her devotion and care have always been a great source of inspiration for me.