Biomedical Engineering Reference
In-Depth Information
In March 2010 the reactions recorded in the UsefulChem notebook were
abstracted into a machine-readable format as part of the Reaction Attempts
(RA) database [87]. In April 2010 the fi rst edition of the RA book was pub-
lished in conjunction with the fi rst archive of the UsefulChem laboratory
notebook and associated raw data fi les [88]. The RA database also started to
abstract reactions from other open notebooks, like the one shared by the Todd
group on the Synaptic Leap [89]. The usefulness of sharing the abstracted
information from open notebooks became clear in June 2010 when attempted
reactions revealed an overlap between the Bradley and Todd groups, allowing
for a very effi cient collaboration and sharing of details about challenges ben-
efi cial to both groups and anyone else with an interest [90]. A Web-based
Reaction Attempts explorer was also created to allow searching by reactant
or product drop-down menus or substructure [91].
25.3.5
Second Life
Long-lasting collaborations can spring from some unusual places. While
exploring the virtual world Second Life as another channel to communicate
open notebook information, a contact was made between two of the authors,
Bradley (JCB) and Lang (AL) [92]. The fi rst collaborative project involved
improving the 3D Second Life molecule rezzer developed by AL so that it
could be used easily by simply supplying a SMILES in the chat box to generate
the molecules with a realistic 3D conformation [93]. This permitted a display
of Ugi products, enoyl reductase, and slides from a recent presentation, all
hyperlinked to either blog posts or laboratory notebook pages for further
details [94]. An effort was then made to index molecules in Second Life on a
wiki [95] .
In June 2007 a collaboration between an extended team resulted in a 3D
animation demo of the docking of a Ugi product into the binding pocket of
enoyl reductase via four hydrogen bond sites [96]. An interactive 3D anima-
tion of the formation of imine—the fi rst step in the mechanism of the Ugi
reaction—was displayed in Second Life in August 2007 [97]. These are power-
ful demonstrations of how sophisticated representations of research within an
open notebook can be leveraged from the contribution of expertise from
several individuals brought together for rapidly implemented applications.
25.3.6
Requesting Collaboration
In March 2006, JCB requested help with disabled instrumentation on the
UsefulChem blog [98]. It is interesting to note that most specifi c open requests
of this type were not directly answered. Most of the collaborations to arise
from the project did so based on a shared overlap of interests, and this often
caused a shift in project direction. Flexibility is of paramount importance when
embarking upon these types of collaboration—all parties need to benefi t. This
experience suggests that open-science platforms primarily based on very
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