Biomedical Engineering Reference
In-Depth Information
Of course, as much biological and chemical information is stored in
relational databases then knowledge of the Structured Query Language
(SQL) is also a key skill for anyone routinely working with such
information. Here again, the availability of free database systems (see
above) provides the opportunity for anyone to explore and teach
themselves without fear of breaking someone else's database. Free SQL
clients such as SQuirrel [33], Oracle SQL Developer [34] and in the
MySQL world, MySQL Workbench [35] and PhpMyAdmin [36], provide
many capabilities for zero cost. Again, the availability of powerful
database management software is incredibly enabling and is another
factor aiding companies whose primary goal is science, rather than
software development.
Finally, data analysis is also a key skill. More and more, a good
understanding of the basics of statistics will help understand the validity
and outcome of the many large-scale analyses now available within
biology. As such, knowledge of tools, particularly the R project for
statistical computing, as well as bioinformatics applications, can be
crucial. If more advanced machine-learning approaches are required, the
Weka [37] system offers an extensive range of algorithms and techniques,
often more than enough to test an initial hypothesis.
10.9 Conclusion
FLOSS fulfi ls many critical roles within OGT that would otherwise
require investment in alternative commercial products. In selecting
FLOSS over these other solutions, there is, of course, a cost element to be
considered, but that is not the whole story. If any FLOSS product did not
meet the required functional criteria then it would not be used; similarly,
if a better commercial product becomes available then this would be
considered. However, besides reducing expenditure on licences, there are
additional advantages from taking a FLOSS approach.
First, if there is a problem, then the very nature of open source software
means that, assuming you have the technical ability, it is possible to see
directly where the problem is. This was experienced directly at OGT
when the format of some NCBI Genbank records changed. The
downstream effect of this was that an application using a BioJava fi le
parser threw an error. Because the code was available it was possible to
fi nd the problem and fi x it locally so the parsing could complete. But
beyond that the fi x could be passed to the developers for incorporation
into the distribution and made available to the whole community. In the
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