Biomedical Engineering Reference
In-Depth Information
review involve many other scientists. Moreover, as most cheminformatics
approaches fi nd patterns and relationships at various levels of detail, using
methodologies which are typically mathematical and are aimed at identifying
correlations rather than physical and chemical cause-effect relations, the
domain fi nds itself once again collaborating with the experimental scientist to
validate the derived models and predictions against new experimental data.
However, as the fi eld has matured, it has become more specialized, and with
more specialization, the nature of those collaborations have changed. A study
could have started as a laboratory scientist doing cheminformatics as a side
project, while the domain later evolved to people specializing in cheminfor-
matics while collaborating with other scientists in the same group and then
later collaborating with other research groups. Nowadays, it is even common
to collaborate with scientists around the world as even the same university
may no longer share the same specialty. The evolution of Internet technologies
resulted in an era of online science.
Fortunately, cheminformatics is at an advantage compared to other sciences.
Data exchange, processing, and analysis are all done electronically, making it
suitable to be scaled up to online science. This chapter will defi ne and detail
the various tools cheminformaticians have at hand to simplify this online
collaboration.
Cheminformatics deals with the aggregation, handling, processing, and
analysis of chemical data. The nature of the chemical data is in principle not
important. However, the history of the fi eld and its separation from quantum
chemistry fi elds bias the domain toward small organic molecules. The patterns
in collaborative applications are, however, independent of the exact nature
of the data. Therefore, we will focus in this chapter on another dimension
to discuss the aspects of collaborative cheminformatics applications: code
development, knowledge handling and data exchange, and collaborative
computation.
The fi rst section will focus on methods involved in the collaborative devel-
opment of cheminformatics software and will discuss the tools modern scien-
tists have to perform this task. The next section will describe recent changes
in which we handle chemical data and knowledge, in particular how the
Internet is changing the way communities create new knowledge bases. The
third section will focus on the aspects of collaborative computing in chemin-
formatics. Finally, the fourth section will describe social aspects of collabora-
tive projects, in particular how collaboration is managed in projects with only
loosely defi ned roles for the various partners.
24.2
COLLABORATIVE CODE DEVELOPMENT
Collaborative code development is a common approach for large software
vendors. For scientifi c software, however, it is less common: New software is
typically started as a Ph.D. or M.Sc. project with a single developer. There are,
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