Biomedical Engineering Reference
In-Depth Information
developers to free themselves of software installation and management and
onerous licensing conditions.
24.4.2
Sharing Computation Specifi cations
A simple example of a “computation specifi cation” is the source code of a
program or even an input fi le for a program. In both cases, the document fully
specifi es what is required to run a program to achieve a desired result. Clearly
there have been many mechanisms to share such specifi cations. However, with
a few exceptions these sharing mechanisms tend to simply collect source code,
for example, in a central repository and let users access it from there. Usually,
there is no metadata attached or associated with the source code, and thus
exploring related cases is diffi cult.
Recently, there has been a signifi cant amount of effort devoted to the
development of “ workfl ow ” or “ pipelining ” tools for chem - and bioinformatics.
These tools encapsulate core cheminformatics tasks such as reading in SMILES,
evaluating descriptors, and so on, in simple graphical elements (usually boxes
and connectors). A user can then arrange sequences of such elements to
perform a task. The graphical user interface (GUI) approach, coupled with the
fact that in most cases such workfl ow tools require no programming knowl-
edge, makes such tools very attractive to experimentalists and other users with
limited programming experience. A number of such tools are available, includ-
ing Pipeline Pilot [78], KNIME [79], and Taverna [80].
Another development around workfl ow tools is the sharing of workfl ow
specifi cations (or “ programs ” ), exemplifi ed by the MyExperiment website
[81], which allows sharing of scientifi c workfl ow of various formats, including
Taverna [80, 82] (see Fig. 24.6) and Bioclipse [45, 46]. MyExperiment is a social
website where scientists can share workfl ow specifi cations, tag them, catego-
rize them, or modify and upload new, improved versions. This makes it easy
to reproduce analyses and potentially improve scientifi c progress.
24.4.3
Online Cheminformatics Computation
It should be noted that these online workfl ow sharing services do require
download of the workfl ows to a local desktop, where they can then be run.
Both Taverna and Bioclipse provide the means to download a workfl ow shared
on MyExperiment.org from within the desktop software, but it is not possible
to run the computation at a remote server unless the workfl ow specifi es that.
However, the ongoing evolution of collaborative cheminformatics is making
this possible and various companies are appearing that develop software that
make it possible to design and run workfl ows via websites.
One example of this approach is Wingu Elements [83], by the Boston start-
up Wingu. This product provides a cloud-based platform for research teams
to defi ne workfl ows, make them available within the collaboration, and then
share the results as shown in Figure 24.7.
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