Databases and Systems

2
genome maps to be built (in some species) without reliance on cumbersome natural
recombination; and high-throughput screening methods which allow the biological
effects of large small-molecule compound libraries to be rapidly assessed. If
genomics at present is using tomorrow’s technologies today, often before all the
kinks have been worked out, numerous groups are hard at work on the technologies
of the day after tomorrow. Examples include protein profiling, or proteomics, which
surveys the protein content of cells and tissues using high-resolution mass
spectrometry; metabolic profiling, which measures the small molecule content of
tissues; cheap polymorphism detection methods; and nanofabricated laboratory-on-achip
technologies that may provide the elusive increases in speed and reductions in
cost that have long been sought for “conventional” genomic technologies such as
automated sequencing.
It is against the backdrop of this breakneck technology development and
mass production of genomic data that the field of bioinformatics emerged. People
had of course been applying computers to biological data for years before the term
was coined, and most of the common algorithms for biological sequence comparison
had been invented by 1980. But it was not until the mid-1990’s that the field acquired
a name, and suddenly became respectable, even fashionable. By 1996 it seemed that
every other issue of Science contained an article bemoaning the desperate shortage of
bioinformaticians in academic and industrial labs (e.g. [ 141).
A crucial parallel development in the larger culture that coincided with the
emergence of genomics and bioinformatics was the explosion of the Worldwide
Web. Vindicating, perhaps, Marshall MacLuhan’s cryptic insight that “the medium is
the message” (or “mass age”), the Web has inserted itself into discipline after
discipline, business after business, unleashing expanding ripples of transformation.
Indeed the Web is one of the few technologies that are developing as fast as
genomics, but the connection between them runs deeper than that. The Web turns out
to be a nearly ideal vehicle for delivering genomic data to the scientific community; it
is hard to imagine what bioinformatics would look like without it.
So what is bioinformatics? Definitions vary with the users of word; related
terms like computational biology are held to be synonyms by some, and by others to
reflect subtle distinctions. In practical terms there are some important distinctions to
be made between the tasks of developing algorithms, of programming databases, and
of curating database content. Computational biology algorithms for sequence
comparison, sequence assembly, sequence classification, motif induction and
recognition, and protein structure prediction have been the subject of several recent
books [7-13] whereas the database system-building and content curation aspects have
received less treatment 2 . These are perhaps the less glamorous aspects of the field,
more lore than art, but these are also the areas where there seems to be a great hunger
²
A noteworthy exception is the annual database issue of Nucleic Acids Research
which each January allows public database providers the opportunity to report on
recent developments in their projects. This book is intended to provide a
complementary resource, with more freedom to explore particular aspects of the
systems in depth.