Biomedical Engineering Reference
In-Depth Information
JavaServer Pages technologies and it is for this that it has been used at
OGT;
■
PHP [32] - PHP is a widely used general-purpose scripting language
that is especially suited for web development as it can be embedded
into HTML. In conjunction with Apache and MySQL, we have used it
extensively to develop our internal web services.
In addition to the free tools listed above, there are also those that require
a commercial licence (but can be free to academic and non-profi t groups).
As this adds to the cost of implementation, each application is evaluated
on a case-by-case basis. If a tool can provide additional 'must-have'
functionality, the investment can often be justifi ed. Below are some
commercial non-FLOSS tools that we have employed:
■
BLAT [33] - the Blast Like Alignment Tool or BLAT is an alternative
to BLAST and is available from Kent Informatics, a spin-out of the
University of California at Santa Cruz (UCSC). BLAT is similar to
BLAST in that is used to fi nd related sequences of interest. However, it
has been optimised for fi nding better matches rather than distant
homologues. Thus, BLAT would be a better choice to use when looking
for sequences that are stronger and longer homologues. Unlike BLAST,
a BLAT query runs against a database that has been pre-loaded into
memory. Coupled with BLAT's 'close-relatives' algorithm, the result is
a search tool that runs very rapidly. In many applications where distant
sequence relationships are not required, BLAT provides a highly
effi cient approach to sequence analysis. Unlike BLAST, however, BLAT
is not free and commercial users require a licence (although it is free to
non-profi t organisations);
■
Feature Extraction - Agilent's Feature Extraction software reads and
processes the raw microarray image fi les. The software automatically
fi nds and places microarray grids and then outputs a text fi le containing
all the feature information. There is currently no FLOSS alternative;
■
GenePix [34] - GenePix from Molecular Dynamics is another
microarray application. It can drive the scanner as well as feature
extract data from the resultant image fi le;
■
GeneSpring - Agilent's GeneSpring is an application to process feature
extraction fi les from microarrays used in gene expression studies. It is
easy to use and has useful workfl ows that make it easy analyse this
type of data. A disadvantage is that the workfl ows hide many
parameters that might otherwise be adjusted within the analysis.
However, performing similar analyses with R is not straightforward
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