Biology Reference
In-Depth Information
FIGURE 7.1
Time line showing biology and Internet milestones side by side. Similar time lines can be
found in many introductory bioinformatics and computational biology courses or in online accounts of
the history of bioinformatics. (Compiled by author from fi eldwork notes.)
concurrent with one another. This sharing requires the daily exchange
of raw DNA data dumps (swap trace fi les of terabyte size) across the
Atlantic. Likewise, large sequencing centers, which are contractually re-
quired to submit their sequences to the appropriate databases on a daily
basis, must often transmit massive amounts of data over the Internet
every night. One computational biologist responsible for such uploads
at the Broad Institute told me that some data dumps had been inter-
preted by Internet administrators as malicious BitTorrent attacks and
subsequently shut down.
One specifi c example of the importance of biology to the Internet
is the story of cgi.pm. In the mid-1990s, at the Whitehead Institute in
Cambridge, Massachusetts, Lincoln Stein was working to publish the
laboratory's physical maps of the genome. Stein needed a quick and
cheap way to retrieve data from a database and display them on a web
page. A few years earlier, Internet developers had created the Common
Gateway Interface (CGI), which provided a language in which host ma-
chines could make requests to the server (to open a fi le on the server, for
example). In 1995, Stein developed a module in the scripting language
Perl called cgi.pm, which permitted information to be passed backward
and forward quickly between host and server using CGI; cgi.pm takes
user input, executes the appropriate operations on the server based on
that input, and creates HTML output. The module became the basis for
creating “dynamic” web pages, transforming the web from a fi xed col-
lection of pages into a space in which pages could generate their own
content depending on user input.
10
The module became one of the most
ubiquitous and widely used scripts on the Internet. It was cgi.pm that
allowed the Internet to be transformed from a static, server-oriented
