Biomedical Engineering Reference
In-Depth Information
Issues
Despite a history of over a decade of international cooperation in sequencing the human genome,
there remain several impediments to realizing the full potential of collaboration in bioinformatics.
Many issues are external to the bioinformatics field, and are tied to the internal politics and
economics of international pharmaceutical companies. In addition, there are several internal issues
associated with establishing and maintaining collaborations. As described in the following paragraphs,
these include platform dependence, security, intellectual property, and economics.
Platform Dependence
There's something to be said for a world in which everyone is limited to single make and model of
desktop computer. For example, if the bioinformatics community standardized on vanilla 1 GHz
Pentium IV computers running Linux, managing networks, creating applications, and sharing files and
applications would be non-issues. However, computationally intensive applications, such as sequence
alignment, might require weeks or months of processing time. Similarly, without a graphics hardware
accelerator card, the rendering of protein structures on the screen would be excruciatingly slow.
Many third-party software packages, including general-purpose office software and utilities, may not
work as expected or at all.
For better or worse, we work in a world dominated by a few computer hardware manufacturers and
operating system developers. As a result, users become accustomed to one kind of hardware or one
set of tools, and come to depend on having the look and feel of a familiar interface available when
they work. For example, to the regular user of a Sun workstation, the Mac's keyboard and mouse
may feel foreign, and the slight difference in the layout of the keys may initially result in an
abnormally large number of typing errors.
Most basic human-computer interface issues associated with platform dependence have yet to be
resolved. This is especially true in a market that attempts to differentiate commodity computer
hardware in terms of personality or even color—factors that don't directly affect the performance or
usefulness of applications running on the computer.
One area in which platform dependence has been addressed is in tool development, especially in
platform-independent programming languages and applications. For example, Java is popular in part
because it's available for virtually every desktop hardware-operating system combination in general
use. As a result, developers aren't limited to a particular hardware platform, but they can easily
migrate an application written in Java from one platform to the next.
Security
Collaboration implies trust and requires a degree of connectivity between workstations and other
devices. Whenever this connectivity takes the form of a wired or wireless connection to the Internet,
internets, or an intranet, it represents a security risk. Every Web server or workstation connected to
the Internet is a potential target for hackers, and wireless devices represent an easy portal of entry
for sophisticated hackers. Although some cyberattacks, such as denial of service, are directed at
specific servers, the greatest threats to the typical bioinformatics lab are computer viruses, worms,
or Trojan horses.
Improving security entails the use of anti-virus utilities, software or hardware firewalls to protect a
network from unauthorized external access, password protection of sensitive documents, and the
ability to train staff on security procedures. A robust security infrastructure is especially critical in
commercial laboratory settings where corporate espionage is a constant threat, and in academic
laboratories working on sensitive projects that may be of interest to those who would use biologicals
as weapons.
