Biomedical Engineering Reference
In-Depth Information
user interactivity are possible with this approach, and performance isn't affected by the potentially
slow-speed Internet connection. The application can use any metaphor, input devices, and user
interfaces within the limits of the operating system, local hardware, programming language, and the
designer's skill and imagination. The other major approach to system architecture (D) is a stand-
alone application, such as RasMol, that uses data from a local database. These data may be
downloaded from local experiments or downloaded asynchronously from the public databases on the
Internet.
Given this range of possible architectures, what remains to be defined are the implementation-
specific capabilities that support visualization of data, such as nucleotide sequence or protein
structures, and the format of the results of data analysis. Due to the wide range of open-source tools
available, the new tools under development, and the additions being made to existing tools, selecting
the best tool for a particular application generally begins with exploring the bioinformatics Web sites.
A summary of the characteristics of the four basic architectures is provided in
Table 5-3
. Note that a
native browser application, such as Map Viewer, generally has high marks for portability and ease of
maintenance. Portability is not a concern because virtually every computer platform is compatible
with Netscape Navigator and/or Internet Explorer. In addition, because the graphics-rendering
program sits on the server, there is nothing to update on the workstation running Map Viewer—with
the possible exception of the Web browser if an application requires a later version than is installed
on the workstation. The downside of this third-part maintenance of the application is that the user
interface is limited to whatever the original designers defined; there isn't an easy way to alter how
data are displayed in the Map Viewer program, for example. Similarly, the performance of Map
Viewer is limited to that of the server, so there is little in the way that be done on the workstation to
increase performance other than assuring a high-speed connection.
Table 5-3. Visualization Program Architecture Characteristics.
User Interface
Flexibility
Architecture
Portability Performance
Ease of Maintenance
Native Browser
X
X
Extended Browser X
X
X
Web-Enabled
X
X
Stand-Alone
X
The extended browser model gets high marks for portability, performance, and user interface
flexibility, and, compared to a native browser application, less than stellar marks for ease of
maintenance. Most, but not all, plug-ins are compatible with every platform that supports a Web
browser. Some plug-ins are optimized for Netscape Navigator and don't perform well or at all with
Microsoft's Internet Explorer. The Chime plug-in, for example, requires a Netscape browser. Moving
from a native browser environment to a plug-in that executes on the local workstation means that
local hardware can be used to improve program performance.
Most of this performance increase is due to support for high-performance OpenGL-compatible
graphics cards. OpenGL is a cross-platform standard (Windows, MacOS 9 and X, Linux, and UNIX) for
3D rendering and hardware acceleration. The underlying architecture of an OpenGL-compatible video
card is usually some variation of that depicted in
Figure 5-20
. An application communicates through
the workstation bus to the controller hardware in the video card that drives a monitor.
Figure 5-20. Interface Display Architecture.
