Biomedical Engineering Reference
In-Depth Information
not based on folders and trashcans, but on molecular biology metaphors such as the Central Dogma,
where chromosomes and genes provide organizational hierarchies in which form and function are
mapped.
Work on interface design in clinical medicine provides one model for how a niche-specific interface
can become the de facto standard. In clinical medicine, the metaphor of a paper medical record is
pervasive. Many clinicians interact with a patient's electronic medical record through the metaphor of
a paper medical chart in which the data are arranged by the patient's chief complaint, medical
history, review of systems, physical exam, and laboratory results and never see or interact directly
with the underlying operating system. Whether a bioinformatics-centric user interface evolves out of
academic or commercial molecular biology laboratories depends on the creativity and resources of
those in the field.
Developing a completely new user interface from scratch is a formidable task. It's easier to extend
current interfaces through commercial utilities or by writing browser extensions, than to specify a
new interface. For example, eXtensible Markup Language (XML), Virtual Reality Modeling Language
(VRML), PHP: Hypertext Processing (PHP), and similar high-level languages can be used to extend
browser functionality to work with manipulating 3D images and to create a new interface metaphor.
Another option is to select from commercial or shareware alternative front ends to desktop and Web-
based applications that use alternative metaphors. TheBrain Technologies, illustrated in
Figure 5-
18
,is but one of many alternatives to the business-oriented desktop metaphor. It uses the metaphor
of a non-hierarchical mesh of linked associations, in which concepts are related to each other through
logical association. For example, a mesh of associations based on the Central Dogma can be
established in which nucleotide sequences are associated with protein structures through an
intermediary link that associates proteins with both 3D structures and with genes that code for the
specific protein.
Figure 5-18. Alternative User Interface. This example of an alternative
desktop and Web browser, TheBrain Technologies Corporation's
PersonalBrain, illustrates how an alternative metaphor can be used to
provide access to computer and Web-based bioinformatics applications and
data.
