Biomedical Engineering Reference
In-Depth Information
in posts on the UsefulChem-Molecules blog [10, 11]. The fi rst comment on the
Experiments blog from a researcher outside the existing group came from a
researcher at the University of Sydney [12], Mat Todd, and provided valuable
insight. This contribution was reciprocated later by promoting the Todd group's
open project on the chemical praziquantel [13]. Other scientists would con-
tinue to periodically comment on later blog posts [14].
By June 2006 it became clear that a blog was not providing the necessary
functions for a laboratory notebook, mainly because version control was not
available [15, 16]. The plan at this time was to record the laboratory notebook
information on the wiki, then copy it over to the Experiments blog when the
experiment was fi nalized. However, in practice, the concept of a “fi nalized
experiment” proved diffi cult to judge and the wiki was simply used as the
actual laboratory notebook. This way errors discovered at any time could be
corrected on the wiki with proper version tracking to determine who contrib-
uted what and when. The use of a wiki for a laboratory notebook also made
it very convenient for mentors to communicate with students by commenting
directly on specifi c sections of a page. The availability of e-mail alerts for any
changes on the wiki facilitated very rapid communication.
With the accumulation of data, more effort was invested into providing
tools for searching. It was deemed important that both the blogs and wikis be
quickly indexed on major search engines. Google Co-op Search allowed for a
very simple way of performing a federated search of all of the UsefulChem
platforms [17] and was also used later for other multiple ONS resources [18].
Google applications would prove to be key for other sophisticated search and
retrieval tools that would evolve over time.
In March 2007 UsefulChem compounds were hosted as part of the eMol-
ecules collection, thereby permitting additional sophisticated services such as
substructure searching [19]. The use of Google spreadsheets in UsefulChem
for data storage and manipulation proved to be another powerful example of
leveraging free hosted resources. Free Google and Sitemeter services also
facilitated the discovery of UsefulChem content via license fi ltering and visitor
tracking, respectively [20]. In August 2007 Collaborative Drug Discovery
(CDD) provided UsefulChem with a free account to store and share assay
results [21]. Neylon's laboratory used another free hosted database applica-
tion, Dabble, to list people involved in ONS [22].
At the end of March 2007, ChemSpider was fi rst used to manage UsefulChem
molecules [23]. A full transition to ChemSpider was completed in June 2007
with the demonstration of substructure searching and the use of the
UsefulChem-Molecules blog was discontinued [24]. This free and hosted
online chemical database would prove to be integral to many projects. The
ability to provide experimental and predicted properties was one of the fi rst
essential functionalities exploited. UsefulChem acquired a subdomain on
ChemSpider in April 2008 and students were encouraged to upload nuclear
magnetic resonance (NMR) spectra of reagents and purifi ed products as open
data [25] .
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