Biology Reference
In-Depth Information
entity into a fl exible, user-centered tool. The notion that the user could
send information over the Internet (for instance, a name, address, and
credit card number) that could then be stored on the server or used to
generate customized HTML pages was crucial for the development of
e-commerce.
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Indeed, the Perl language more generally has had a profound ef-
fect on both the web and biology. In the early days of the web, Perl
played the dominant role in CGI programming, which allowed data to
be passed from a client machine to a program running on a server. Has-
san Schroeder, Sun Microsystems' fi rst webmaster, remarked, “Perl is
the duct tape of the Internet.”
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Its ability to “glue together” programs
written in a variety of other languages made Perl an ideal tool for the
web developer, webmaster, or systems administrator. Similarly, it was
Perl's ability to act as an adhesive between different sorts of programs
that allowed it to “save the Human Genome Project.” As Stein relates,
the various labs working on sequencing the human genome each had
their own independent methods of processing their data, so the resulting
sequence data existed in a variety of incompatible formats.
Perl was used for the glue to make these pieces of software fi t
together. Between each pair of interacting modules were one or
more Perl scripts responsible for massaging the output of one
module into the expected input for another. . . . Perl has been
the solution of choice for genome centers whenever they need
to exchange data, or to retrofi t one center's software module to
work with another center's system.
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Indeed, Perl became such a popular tool for biological work that de-
velopers at major genome centers created an open source community
(called the BioPerl Project) for the purpose of developing and sharing
Perl modules useful to biology. The ubiquity and importance of the Perl
language in the development of the Internet and of the HGP shows that
both projects faced similar obstacles that could be overcome with simi-
lar tools. Specifi cally, Perl provided ways in which small and powerful
software components could be seamlessly linked together in order to
facilitate the smooth transfer of data.
Bioinformatics and the Internet continue to face similar problems
and continue to develop in parallel. In particular, the futures envisioned
for the Internet remain deeply intertwined with efforts to understand
biology, and especially the human genome. Writing about the “past,
present, and future” of the web in 1996, Tim Berners-Lee looked for-
