Bioviz is a project of the Loraine Lab at the University of North Carolina at Charlotte.
The goal of Bioviz is to develop and deploy useful visualization software for bioinformatics and genomics. Currently, we use this site to display and deploy data for our collaborators and colleagues at UNCC and beyond.
We are also developing a public data repository and visualization software server for plant genomics data. For the visualization front end, we are using the Integrated Genome Browser, a free and open source desktop genome browser developed as part of the Genoviz project.
To try out our very experimental PlantIGB prototype, click here. (By very experimental, we just mean that some features, such as the "load sequence in view" button, don't yet work properly. We hope to support this feature very soon, pending development of "back end" data servers.)
Great visualization software stimulates one's creativity, suggests new and exciting avenues for research, and, of course, exposes patterns in data that one would be unlikely to find from perusing data presented as straight text. Writing great visualization tools is an art as well as a science, and, unfortunately, people who have the skill and inclination to do it are quite rare. And people who are willing to share the fruits of their labor free of charge are rarer still! So if you try out some of the following free tools and find you like them, please be sure to let the developers know. And if you have some recommendations to make yourself, please let us know.
TableView, written by Jim Johnson at the University of Minnesota, lets you load tabular data via the Web (using a URL) or from a local file. It has many features, including the ability to click points on scatter plots (such as outliers) and see the corresponding rows in the TableView light up. And of course, you can do the reverse, as well. It is particularly handy for visualizing co-expression data. It's written in Java, and Jim has set up a Java Web Start page you can use to download and launch the program.
JalView is an alignment viewer and editor, originally written by Michelle Clamp and now lovingly maintained by a team at the University of Dundee. They also provide a Java Web Start page for it.
Matrix2png - an incredibly useful tool for generating heatmaps written by Paul Pavlidis' group. It's written in C and is also a great tool for visualizing co-expression data...and many other types of matrices, as well. Paul's Web site has some great screenshots showing examples of how various researchers have used it over the years.
Eric Blossom, of Blossom Associates West, who set up the first version of the IGB Java Web Start page on Bioviz. Thank you Eric!
Gregg Helt and Ed Erwin of Affymetrix, developers of the Integrated Genome Browser software program, among others. And thank you also to Affymetrix for the open source release of our favorite software.
We also gratefully acknowledge the UAB School of Public Health IT group for providing Internet connectivity for the Bioviz and Loraine Lab Web sites during our recent move from UAB to UNCC.