Libby Shoop's Research Project: Integrated Genome Data Exploration Tools

Several Macalester students and I have created a system of Java tools that enable genome researchers to explore and visualize different types of data at the same time. To make the data exploration easier, we enable the users to pass sets of genes from one tool to another, and those gene are then immediately visualized in the tool that received the genes. We have built the system so that additional Java tools can be incorporated. In fact, two of the tools we have in the system were not originally built by us, but are available as open source.

The tools we currently have integrated into the system are:

• The Genome Traffic Controller (GTC), which keeps track of the user's sets of genes and controls the execution of each tool and the passing of sets of genes from one tool to the next.
• A Genome Viewer (AGV), which is a simple Genome Viewer that distinguishes itself by showing a high-level view of all chromosomes at once and enables zooming in to several regions of the choromosome simultaneously.
• GoGet, which enbles querying the Gene Ontology Database for genes of interest from particular genomes.
• A Tree Viewer (ATV), a phylogenetic tree viewer maintained by Christian Zmasek, http://www.phylosoft.org/.
• (Microarray) Java Tree View, a tool for viewing clustered Microarray data, by Alok Ito, http://jtreeview.sourceforge.net.

The AGV tool currently can access two genomes, Arabidopsis thaliana and Medicago trucatuala, via a distributed annotation service (DAS) that we maintain.

News and Notes

Contributors

Many thanks to the following people who made significant contributions to this project:

• Nevin Young, Ph.D., University of Minnesota
• Steven Cannon, Ph.D., Iowa State University
• Ethalinda Cannon, Iowa State University
• Getira Onsongo, currently at University of Minnesota, formerly Macalester College, '04
• Paulo Casaes, Macalester College, '04
• Daniel Feldman, currently at University of Minnesota, formerly Macalester College, '06
• Nyalleng Moorosi, currently at University of Minnesota, formerly Macalester College, '06
• Methawat Chanla, Macalester College, '07
• Lars T. Johnson, Macalester College, '07
• JenHao Cheng, Macalester College
• Bernd Verst, Macalester College