NATIONAL SCIENCE FOUNDATION
TOKYO REGIONAL OFFICE
The National Science Foundation's (NSF) Tokyo Regional Office periodically receives and disseminates reports on research developments in Japan that are related to the Foundation's mission. It also provide occasional reports on developments in other East Asian Countries (http://www.twics.com/~nsfasia/as-reports.htm).
These reports present information for the use of NSF program officers and policy makers; they are not statements of NSF policy..
Special Scientific Report #01-10 (December 10, 2001)
GENOME VISUALIZATION AND NAVIGATION TOOLS
The following report was prepared by Mr. Andrew G. Palmer, a graduate student in the Department of Computer Sciences at the University of Wisconsin, Madison. Mr. Palmer was a participant in the 2001 Summer Programs in Japan, co-sponsored by the National Science Foundation and Japan’s Ministry of Education and Science (Monbukagakusho). He conducted his research under the direction of Dr. Minoru Kanehisa of the Institute for Chemical Research at the University of Kyoto. Mr. Palmer may be reached at agpalmer@cs.wisc.edu.
Research Description
I Explored designs for web-based computer graphical analysis tools for genome data. The tools are web-based so they may be publicly used via a browser and the world-wide-web. The tools are graphical to provide rich visualization of the data and a robust set of navigation controls. The tools provide a powerful means to search the data. The results would be presented in both a graphical format and table format. The tools would be scalable for use with numerous genomes.
Research Activities
My work at the Kanehisa Laboratory within the University of Kyoto’s Institute for Chemical Research focused on improving the design and implementation of my visualization tool through four tasks: First, I moved the data from flat files to a Postgresql database. Second, I added oligo and high resolution genome array expression data to the set of genome data. Third, I created a means of accessing this data publicly via the World Wide Web. Fourth, I focused on improving the graphic user interface of the tool.
Moving the data from flat files to a Postgresql database involved designing, constructing and populating a table for each data entity. Accessing this database via the World Wide Web required creating a public web user account and granting read permissions to the appropriate tables. I built Java JDBC readers for the tool to then access this database. I built the implementation of the tool so that it could be run as a stand alone application, or as an applet in a web page.
I broke the design of the tool into these groups: The Genome classes, the Genome Graphical Node classes, the SQL classes, and the Application classes. The Application classes included a GUI class with a Query GUI Class, Navigation GUI class, Table GUI class and a Status GUI class. The Application classes also included a DataManager class and a Graphical Node Manager class. The improvements to the Navigation GUI panel included the addition of more sophisticated view modes: A 'Free Transformation' View using the mouse and keyboard, A 'Fit in Window' view, A 'Fit Height' view, and a 'Fit Actual Size' view. Added navigational modes: 'Step Scale In' mode, 'Step Scale Out' mode, 'Horizontal Translation' mode, and 'Free Translation and Scale' mode. Added changing cursors to indicate View Mode.
Perspectives on Research After This Program
The fellowship provided by the Summer 2001 Monbukagakusho Summer Program: Research Experience Fellowship for Young Foreign Researchers with the Kanehisa Laboratory in the Bioinformatics Center of the Institute for Chemical Research at Kyoto University has been a fantastic experience and a worthwhile endeavor for me. I've had an extraordinary summer, both in and out of the laboratory. I feel fortunate to have been a participant. I would like to thank the Japan Ministry of Education, Culture, Sports, Science and Technology and the United States National Science Foundation for selecting me as a participant for the Monbukagakusho Summer Program and for their support throughout the summer. I would like to thank Dr. Minoru Kanehisa and the Kanehisa Laboratory at the Bioinformatics Center of Kyoto University for hosting me for my fellowship and for their great hospitality. I very much enjoyed working with them and I look forward to collaborating on future projects.