Representation and visualization of genetic regulatory networks

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (leaves 61-65).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.by Dacheng Zhao.M.Eng