Biomedical Engineering Reference
In-Depth Information
they represent the convergence of computing, communications, and molecular biology. The Web
continues to serve as the communications vehicle for researchers in working with genomic data,
allowing research scientists to submit their findings to online databases and share in the findings of
others. The Web also provides access to a variety of tools that allow searching and manipulation of
the continually expanding genomic databases as well. Without the Web, the value of the Human
Genome Project would have been significantly diminished.
By 1994, the Web was expanding exponentially because of increased public interest around the time
the first genetically modified (GM) food, Calgene's Flavr Savr™ Tomato was on the market. Cloning of
farm animals followed two years later with the birth of Dolly the sheep—around the time the DVD
was introduced to the consumer market.
At the cusp of the 21st Century, the pace of progress in both computer science and molecular biology
accelerated. Work on the Great Global Grid (GGG) and similar distributed computing systems that
provide computational capabilities to dwarf the largest conventional supercomputers was redoubled.
By 1999, distributed computing systems such as SETI@home (Search for Extraterrestrial
Intelligence) were online. SETI@home is a network of 3.4 million desktop PCs devoted to analyzing
radio telescope data searching for signals of extraterrestrial origin. A similar distributed computing
project, Folding@home, came online in 2001. It performed molecular dynamics simulations of how
proteins fold. The project was started by the chemistry department at Stanford University. It made a
virtual supercomputer of a network of over 20,000 standard computers.
Like most distributed computing projects, SETI@home and folding@home rely primarily on the
donation of PC processing power from individuals connected to the Internet at home (hence the
@home designation). However, there are federally directed projects underway as well. For example,
the federally funded academic research grid project, the Teragrid, was started in 2001—around the
time Noah, the first interspecies clone and an endangered humpbacked wild ox native to Southeast
Asia, was born to a milk cow in Iowa. This virtual supercomputer project, funded by the National
Science Foundation, spans 4 research institutions, providing 600 trillion bytes of storage and is
capable of processing 13 trillion operations per second over a 40-gigabit-per-second optical fiber
backbone. The Teragrid and similar programs promise to provide molecular biologists with affordable
tools for visualizing and modeling complex interactions of protein molecules—tasks that would be
impractical without access to supercomputer power.
On the heels of the race to sequence the majority of coding segments of the human genome—won by
Craig Venter's Celera Genomics with the publication of the "rough draft" in February of 2000—IBM
and Compaq began their race to build the fastest bio-supercomputer to support proteomic research.
IBM's Blue Gene is designed to perform 1,000 trillion calculations per second, or about 25 times
faster than the fastest supercomputer, Japan's Earth Simulator, which is capable of over 35 trillion
operations per second. Blue Gene's architecture is specifically tuned to support the modeling,
manipulation, and visualization of protein molecules. Compaq's Red Storm, in contrast, is a more
general-purpose supercomputer, designed to provide 100 trillion calculations per second. As a result,
in addition to supporting work in molecular biology, Red Storm's design is compatible with work
traditionally performed by supercomputers—nuclear weapons research. Interestingly, IBM and
Compaq are expected to invest as much time and money developing Red Storm and Blue Gene as
Celera Genomics invested in decoding the human genome.
As demonstrated by the timelines in biology, communications, and computer science, the fields
started out on disparate paths, only to converge in the early 1980s. Today, bioinformatics, like many
sciences, deals with the storage, transport, and analysis of information. What distinguishes
bioinformatics from other scientific endeavors is that it focuses on the information encoded in the
genes and how this information affects the universe of biological processes. With this in mind,
consider how bioinformatics is reflected in the Central Dogma of molecular biology.
