Biomedical Engineering Reference
In-Depth Information
As a communications device, not only has the computer helped researchers craft more journal
articles in less time than at any other point in history, but an increasingly large proportion of
academic research information appears online. Up until the mid-1990s, newly discovered nucleotide
sequences from human and other species of DNA were published in printed journals, requiring that
researchers interested in using computer techniques to explore the sequence either key in the
sequences by hand or use optical character recognition (OCR) systems to automatically capture the
printed sequences and translate them into in machine-readable form. Today, no researcher would
think of consulting a printed journal for a nucleotide sequence, but would immediately turn to either
one of the numerous public databases on the Web or one of the value-added commercial databases.
Furthermore, if a printed journal article isn't referenced by one of the electronic databases, such as
PubMed, then the chances of the article ever being read in any form are low.
As computational devices in bioinformatics, computers are used for tasks that range from searching
for nucleotide sequences and visualizing protein folding patterns to simulating complex 3D protein-
protein interactions, for applications ranging from drug discovery to biomaterials research and
development. As an example of computer processing power focused on numeric computation in
bioinformatics, consider that Celera Genomics' network of 800 Compaq AlphaServers has the capacity
to compare up to 250 billion genomic sequences per hour generated by its hundreds of robotic gene
sequencing machines. Even lesser-endowed companies and academic centers are creating high-
performance Beowulf clusters for bioinformatics work. These massively parallel systems that are
constructed from dedicated PC hardware are generally affordable and available to anyone.
Researchers at another pharmacological powerhouse, GlaxoSmithKline (GSK), are studying how
individual variations in the genetic code cause adverse drug reactions in some patients. To pursue
this research, GSK partners with biotech research firms who store clinical data from drug trials and
correlate it with the patient's genetic information to create a genetic profile of patients at risk.
Similarly, clinicians with the Mayo Clinic in Minnesota are working with researchers to identify gene
markers that indicate which patients should respond to specific anticancer therapy. Elsewhere,
pharmaceutical research firms are using genetic traits to predict whether a patient will respond to
therapy as well as the likelihood of serious side effects. Several biotech startups are developing
panels of DNA tests that will allow clinicians to quickly determine how patients metabolize drugs so
that dosage regimens can be tailored to their individual metabolism.
All of these activities revolve around database technology. For example, both communications and
computation operations in bioinformatics depend on data that have to be maintained. Electronic
databases maintain data in a persistent, non-volatile form that allows operations to be repeated and
compared with other operations, with the results communicated to other researchers and developers.
The electronic database—a file composed of records, each containing fields together with a set of
operations for searching, sorting, recombining, and other functions—is the silicon, plastic, and iron-
oxide equivalent of the experimenter's private notebook, and the basis for electronic publishing to the
scientific community.
As an illustration of how central databases are to the molecular biology research and development,
consider a sampling of the public bioinformatics databases listed in
Table 2-1
. Perhaps the best-
known of the hundreds of DNA sequence databases accessible through the Internet are the
international nucleotide sequence database collaborators GENBANK, supported by the National Center
for Biological Information (NCBI), the DNA DataBank of Japan (DDBJ), and the European Molecular
Biology Laboratory (EMBL). Another major database, PubMed, which is maintained by the U.S.
National Library of Medicine, is a key resource for biomedical literature.
Table 2-1. Public Bioinformatics Databases Accessible via the Internet.
Database Type
Example
Note
