Visualization of scientific data is something I am passionate about. During my Ph.D work on long trajectory integrators I produced an OpenGL 'Orrey', a representation of the Solar System, with graphics supplied by NASA 'wrapped' onto the planets. After working on the Folding at Home OpenGL viewer I decided to pursue the idea of embedding the viewer into a webpage to illustrate our Normal Mode Langevin paper. The project, a joint effort between myself and James Sweet at Stafford University in UK, has now grown to be a general purpose viewer visualizing a number of exciting models. These range from Molecular Dynamics to Social Networking.



Basic Viewer.

We have produced a Java Molecular Viewer using the JOGL OpenGL bindings. This allows us to observe
simulations that are running remotely, and can be seen in action on the NML website. It is also used in
the Grid Heating effort at the Greenhouse conservatory in South Bend, IN, to show the scientific efforts
being used to heat the conservatory.


The viewer is also available in MDLab. MDLab is a multi-platform user-friendly environment for prototyping
molecular dynamics simulation protocols and numerical methods, built with the scripting language Python.

Advanced Viewer project.

We have extended the Molecular Viewer to generate a general purpose 3D viewer which can be easily targeted at new projects. The Advanced Viewer supports 3D rendering using equipment such as the Circularly Polarized Screen at CRC or simple using Red/Magenta anaglyphs. In addition to the encapsulation of a rich set of viewer features, since the viewer is written in Java it can be embedded in a webpage as an Applet. You can see the CRC Cyberinfrastructure group viewing a Fibrin Network on the 3D equipment at this link:  Cyberinfrastructure group viewing a 3D visualization.

The viewer has been targeted at visualization projects including Blood clots and Fibrin Networks with Mark Alber's group (ND), Molecular Dynamics with Jesus Izaguirre's group (ND), Social Networks with Zoltan Toroczkai's group (ND) and Microtubule Simulation with Holly Goodson's group (ND).

Faruck Morcos has documented the Fibrin and Phone network development in his networktrekker website.

Social Networks (Click to see movie)


Fibrin Network (Click to see movie)

FibrinFibrin 3D

Molecular Dynamics


3D representations, anaglyph (left) and the format for CRC 3D screen (right).

MD3d1 MD3d2


Publication Quality Output.

We have now added Ray Tracing for high quality output, using Tachyon.

Ray traced rolling platelet