Biomedical Engineering Reference
In-Depth Information
General-Purpose Technologies
The bioinformatics research community is characterized by cooperation in the sharing of data and in
application development. Thanks to the efforts of thousands of researchers in laboratories around the
world, there are libraries of bioinformatics-specific applications that are freely shared among
members of the community. Many of these applications deal with visualization, given the
overwhelming need to have an intuitive means of manipulating the vast amounts of molecular
biology data being generated daily worldwide.
Many general-purpose data-analysis programs provide reasonable visualization capabilities that can
be used in bioinformatics work. The challenge is identifying a proprietary or open-source software
package that either accepts standard bioinformatics data formats or that uses a utility to convert
bioinformatics data into a format suitable for the package.
When it comes to hardware, few laboratories can afford high-end, dedicated visualization
workstations from Silicon Graphics and other manufacturers, much less develop custom hardware to
supplement their visualization needs. The problem with high-end commercial visualization
hardware—from 3D or stereo goggles, data gloves, 3D displays, and haptic devices—is a lack of
standards. A visualization system designed around a particular model of stereo goggles likely won't
work with other hardware because the proprietary software drivers may require a specific operating
system and the display drivers may be incompatible with displays from other manufactures. As a
result, sharing research findings with others is more difficult. The more standard the general-purpose
hardware and software used to support visualization in a laboratory, the more easily the system can
be shared with others. In addition, using a general-purpose tool shifts the maintenance and
standards challenge to the hardware vendors, allowing R&D teams to focus on their own work.
A common approach taken by software developers in aiding the visualization of complex molecules is
to create a stereo pair that can be printed or viewed on a computer screen. This low-tech alternative
to stereo goggles, most of which work by opening and closing an LCD shutter on either of the two
lenses in concert with the display, is based on the cross-eyed technique. If you hold this topic a
comfortable reading distance from your face and stare at the point between the two proteins while
crossing your eyes, you should be able to mentally fuse the two images, differing in only a few
degrees of perspective into one single 3D structure. For example, the stereo pair in
Figure 5-22
illustrates a cross-eyed stereo pair of Deoxy Hemoglobin. Because the computational load of
stereoscopic rendering is approximately twice that of a single image, rendering times can be painfully
long.
Figure 5-22. Cross-Eyed Stereo Pair of Deoxy Hemoglobin Created with
RasMol. To view the molecule in stereo, with the image about 10 inches
from your face, stare at the area between the two molecules and cross your
eyes until a third image forms in the center of the two original molecules.
The original images will remain visible, but will be located in the periphery
of the visual field.