Biomedical Engineering Reference
In-Depth Information
Greasemonkey Mozilla extension [60] and later by the Ubiquity Mozilla
extension [61]. A userscript is simply a small JavaScript program that runs on
the client browser and can modify a given Web page before it is displayed to
the viewer. In other words, given permission to do so, a userscript can com-
pletely rewrite a Web page in any way deemed appropriate and necessary to
the task at hand. This opens up exciting possibilities in annotating Web content
and linking Web content to arbitrary data sources. A variety of userscripts for
cheminformatics have been described by Willighagen et al. [62]. For example,
when viewing a Web page describing chemistry, a userscript can be written to
take the text and run it through a chemical entity recognition tool (such as
OSCAR3 [63]) and then highlight terms that were recognized. Such a script
can be further enhanced by not only highlighting recognized terms but also
inserting hyperlinks to chemical databases such as PubChem or ChemSpider.
Another userscript application described is to display the three-dimensional
(3D) structures of molecules when browsing PubChem Web pages. Previously,
PubChem had not provided 3D structure information, while Indiana University
had separately generated a single low-energy conformer for 99% of PubChem
and stored them in an independent database. A userscript was implemented
that when run on a PubChem compound page would identify the compound
ID and retrieve the corresponding 3D structure (if available) from the Indiana
University database and then display it in a Jmol window. Key to the func-
tionality of many cheminformatics userscripts is the use of freely accessible
cheminformatics Web services (Section 24.3.1) and databases.
24.4
COLLABORATIVE COMPUTING
The development of the necessary infrastructure and tools to link knowledge
bases is a fundamental requirement for effi cient collaborations. The previous
sections have highlighted a variety of efforts in these areas. While it is true
that collaborative efforts (in any fi eld) are primarily a function of social
interactions, it is important to remember that collaborations need not be
directly between individuals. Rather, they can also be mediated by software.
From this point of view, there have been a number of developments in the
last few years that allow individuals unrelated to each other in terms of formal
collaborative agreements to interact with each others' resources. But such
interactions do not necessarily have to involve remote resources. Instead, a
collaboration could also be in the form of shared specifi cations. That is, indi-
viduals could collaborate on the specifi cation of a process or program, which
would then be run locally using each collaborator's own resources. Finally, to
achieve these types of collaborative efforts, technologies to support these are
necessary. Many of these are well established, including mailing lists and chat
systems, whereas a number are more recent and include service registries.
The following sections discuss these facets of collaborative computing in more
detail.
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