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VisArray Project Gallery

VisArray Project Gallery


Folding@Home/Protomol visualization client:

The F@H/Protomol client connects to either a Folding@Home core or an instance of Protomol using local or remote sockets. It is written in Java using JOGL, the OpenGL bindings for Java, and can be run as an application or as an applet for embedding in web-pages. The viewer can also read DCD trajectory files and display the dynamic trajectory. Output is generally rendered to the screen and includes 3D rendering either via hardware or using anaglyphs (Red-Magenta). The output can be Ray-Traced to an image file using the Tachion rendering engine. The picture illustrates a BPTI protein rendered as an anaglyph, this simulation can be viewed here if you have Javascript enabled (or by clicking the 'Launch Viewer' button). This is a collaboration with the Pande Group at Stanford University.

Architecture Visualization:

Preliminary investigation with Drs. Krupali Uplekar, Mark Schurr, Karla Cruise and Paul Turner on the visualization of architecture objects from point cloud data and high resolution photographs.

Digital Visualization Theater for viewing data:

One of the outcomes of the Summer REU student programme at CRC has been to target the Digital Visualization Theater (DVT or dome) facility at Notre Dame as an output device for the VisArray framework. This has been a collaboration with Dr. Keith Davis who is the director of the DVT and who has allowed us development access to the equipment. While still in an early development phase, the VisArray DVT output module has been demonstrated as a plugin to the controlling SkySkan software. The actual viewer software then uses either a local or remote sockets connection to render the data and control the view. This introduces the possibility of controlling the DVT from the front of the theater and using remote facilities, such as HPC, to generate the numeric data to render (for example running molecular dynamics or fluid dynamics packages on clusters).

3D X-ray (CT) scan/Photographic surface rendering:

Work in progress with Matt Leevey of the Integrated Imaging Facility at Notre Dame and Keith Davis of the Digital Visualization Theater (DVT) to bring the visualization of CT scans to the DVT, coupled with high resolution photographic rendering of the specimen surface.

Social Networking, phone network analysis:

The phone network analysis project takes data on call connections within a sub-domain of a phone network and clusters them by using a force based algorithm. The data is extracted from the iCENSA network center database and the edges (calls) connecting nodes (people) are weighted according to the number of calls, the nodes are positioned at random on the surface of a sphere and are then moved dynamically by considering the weighted edges to represent springs. This was a collaboration with Faruck Morcos (formerly at Notre Dame) and Dr. Zoltan Toroczkai, director at iCENSA. A website detailing this research can be found at

Fibrin network viewer:

The Fibrin network project is a collaboration with Dr. Mark Alber (Biocomplexity group at Notre Dame), Dr. Alisa Wolberg (UNC School of Medicine) and Dr. Danny Chen (Computer Science at Notre Dame) and has allowed us to to take z-stack images of real fibrin networks and produce network representations giving node xyz positions and the thickness of the connecting fibrin fibers. These networks can then be displayed for side-by-side comparison or analysed to estimate their mechanical properties.

Great Books project:

The viewer has been incorporated into the Great Books project in collaboration with Eric Lease Morgan, head of the Digital Access and Information Architecture Department at Notre Dame. An example of the process was to generate a semantic network for Shakespeare's work. The nodes then represent the great idea concepts in the article, two concepts are linked if they exist in the same sentence and within a given distance. The resulting network is then clustered using a force-based algorithm to show the relationship between words that were selected.


The Orrey project was started during Dr. Chris Sweet's Ph.D work on long trajectory integrators using a representation of the Solar System, with graphics supplied by NASA 'wrapped' onto the planets. The application was used to test the stability of various numerical integration methods over a simulated period of 1 billion years in collaboration with Dr. Ben Leimkuhler of Edinburg University. The project was subsequently used as a GPU test bed by James Sweet of Stafford University UK.