Downloadable Software, by my collaborators or me

Variant View

by Joel Ferstay. Vis tool for analyzing genetic sequence variants. Released August 2013.

Vismon

by Maryam Booshehrian. Visual tool for fisheries management data analysis. Version 1.0 released January 2010, latest version 2.5.1 released August 2012.

DimStiller

by Stephen Ingram. Visual tool for dimensional analysis and reduction. Released March 2010.

MulteeSum

by Miriah Meyer. Exploration tool that supports the comparison of multiple gene expression data sets defined both spatially and temporally. Released October 2010.

Pathline

by Miriah Meyer. Tool that visualizes temporal gene expression data over multiple molecular pathways and across multiple species. Released June 2010.

Mizbee

by Miriah Meyer. Browser that enables analysis of comparative genomics data through visualization across multiple scales. Released December 2009.

Glimmer

by Stephen Ingram. GPU and CPU versions of fast and robust multilevel multidimensional scaling algorithm. Released July 2008.

GrouseFlocks, Grouse

by Daniel Archambault. Multilevel graph hierarchy exploration tools, built on the Tulip framework. Released July 2008.

SPF

by Daniel Archambault. Quasi-tree graph layout, built on the Tulip framework. Released May 2008.

TopoLayout

by Daniel Archambault. Feature-based multilevel graph layout, built on the Tulip framework. Released May 2008.

Cerebral

by Aaron Barsky. Cytoscape plugin for compartmentalized network layout, for instance using subcellular localization annotations, and comparing quantitative data from multiple experiments. Version 2.0 (compatible with Cytoscape 2.6) released May 2008. Version 2.8.2 (compatible with Cytoscape 2.8.2) released January 2012.

SequenceJuxtaposer

by James Slack and Kristian Hildebrand. SJ is open-source software for browsing and comparing gene sequences, using accordion drawing. Version 1.2 released Feb 2005.

TreeJuxtaposer

by James Slack, Kristian Hildebrand, Tamara Munzner, Francois Guimbretiere, Li Zhang, Yunhung Zhou. TJ is open-source software for browsing and comparing trees. It uses accordion drawing, an information visualization technique that features rubber-sheet navigation and the guaranteed visibility of marked areas. It was specifically designed for biologists who want to compare phylogenetic or taxonomic trees, but can work for any hierarchies. It can handle trees of up to several million nodes.

[Download source or binaries (Mac, Windows, Linux)]

HypViewer 1.0

by Tamara Munzner. HypViewer is the 3D hyperbolic module used in Site Manager below, now available for free noncommercial use. Contact SGI for licensing for commercial use.

[Download source or binaries (Linux, Irix, Windows)]

Site Manager 1.1

by Alan Braverman, Greg Ferguson, and Tamara Munzner. Site Manager was free software from Silicon Graphics for webmasters and content creators. It included a 3D hyperbolic view of the link structure of the target web site. That module was an implementation of the layout described in my InfoVis 97 paper. Version 1.1 includes the guaranteed frame rate drawing algorithm described in a Graph Drawing 98 paper.

[Download] (No longer available; was packaged with Irix 6.)

Site Manager User's Guide Documentation still available.

Geomview

by Stuart Levy, Tamara Munzner, Mark Phillips, and others. I was one of the core team responsible for design, implementation, documentation, distribution, and maintenance of Geomview, a public domain 3D interactive visualization package with over one thousand registered users. We encourage people to let us know how they use our tools, and have heard back from hundreds of them in a wide variety of domains, including topology, computational geometry, computer graphics, robotics, medical imaging, nuclear physics, mechanical engineering, civil engineering, biomechanics, spacecraft design, computational electromagnetics, and seismology.

[Download] version 1.8

[Download] previous versions from former Geometry Center home

Triangle Tiling

by Tamara Munzner, Charlie Gunn, Stuart Levy, and Olaf Holt. The Triangle Tiling museum exhibit allows people to explore the connections between symmetry groups, tiling, the Platonic and Archimedean solids, and non-Euclidean geometry through interactive 3D graphics. I adapted research software originally written by Charlie Gunn for museum use with Stuart Levy and Olaf Holt. The program features mathematical concepts such as the relationship between Platonic and Archimedean solids, duality, and spherical geometry. The adaptation was done in collaboration with the Science Museum of Minnesota, where it is on exhibit. The software was also shown at ``The Edge'', the interactive installation showcase at SIGGRAPH 94. There's an article about it in the Geometry Forum archives.

Download:

• OpenGL SGI binaries
• IrisGL SGI binaries (Irix 4.x or earlier)
• Mac and Windows binaries ported by Jeff Weeks, who added additional functionality and named it KaleidoTile.
• Linux port created by Pedro Ribeiro for the Atractor exhibit in Lisbon. This version is also multilingual: you can switch the interface between English, French, German, Italian, Portuguese, and Spanish. (Note: if you have troubles running on your machine, try downloading Geomview 1.8 and substituting that bin/gvx for the one in this distribution.)

WebOOGL

by Tamara Munzner. I was involved in the VRML 1.0 standards process starting in 1994, when integrating 3D with the Web was a hot new topic. The WebOOGL software was a proof of concept to back our format proposal. After SGI Inventor-based proposal won the vote (ours came in second), we retro-fitted the WebOOGL software into a quasi-compliant VRML 1.0 viewer. Development has not continued since I left the Geometry Center in 1995, and it is rather unlikely that any 2.0 support would ever be added. My mathematical zoo page has seen a lot of traffic since it was part of the original content pages highlighted during the first big VRML browser release in March 1995. It contains files in both VRML and the WebOOGL native 3D format.

Download if you're curious, but this software is not currently supported.

Caidants

by Tamara Munzner and Eric Hoffman. The CAIDA toolset for network drawing. Some aspects of it are described in a paper on visualizing the MBone. These tools were used to create a series of short videos, including the Planet Multicast video. The toolkit can also be used to create Web pages like the MBone or the NLANR caching hierarchy daily pages, which contain automatically generated 3D and 2D snapshots of the day's data. Released October 1996.

Download if you're curious, but this software is not current supported.