Biomedical Engineering Reference
In-Depth Information
4.10 Perspective
As previously mentioned, the 'omics technologies are developing at a
rapid pace and the open source world is playing a valuable role in plugging
the gap between newly developed academic methods and commercial
vendors' software. Many innovative and imaginative software packages
are being developed, indeed since fi rst writing this chapter the author has
become aware of three more metabolomics packages namely MAVEN
[55], R 'Metabonomic' Package [56] and Automics [57], the former for
LC-MS and the latter two for NMR metabolomics.
Some issues with open source are diffi cult to use interfaces, experimental
or buggy features, fragmentation of effort and poor availability of
training materials. However, the growth of video-based training is
beginning to improve the ease of use.
Another concern is the abandonment of projects. However, unlike
commercial software, the source code is available so it is always possible
to inspect, revive and adapt code which is no longer developed. Security
is another concern, but as the code is under open scrutiny there should be
less reason to fear open source than closed software.
One area that is frequently talked about, especially by commercial
vendors, is the 'lack of technical support' with open source software. In
our experience we have found completely the opposite. The open source
community is very responsive to queries and more often than not bugs
are fi xed within days rather than the often months or years taken by
commercial organisations. Active contribution to the projects also
generates a lot of goodwill and need not be limited to programming skills
as documentation and tutorials are highly valued.
Quite where the rise of open source in science leaves commercial
software vendors is an interesting question. Having worked both in the
software business and as an end user in industry, I can see advantages and
disadvantages to both open and closed source products. The value of
easy-to-use, well documented, validated and tested products that
commercial vendors offer may often be underestimated. High licence fees
may not look so high after considering the extra time needed to implement
and learn less well-documented products (discussed in more detail by
Thornber in Chapter 22). However, these costs are frequently hidden so
that free open source packages may look very attractive from a budget
holder's point of view. Also, the ability to customise and tailor software
exactly to your own needs is a big benefi t that is seldom available with
commercial products.
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