Grid Security - Grid Computing: Infrastructure, Service, and Applications - page 319

results from homosapiens and barley , for example. We note that at the gene
name level, however, it is often the case that common gene name clashes
do exist across species. To support this basic metadata querying, the
GEMEPS project implemented a simple user-oriented portlet that allows
for a variety of these kinds of information to be used for querying over
available (subject to authorization privileges) datasets as indicated on the
left of Figure 12.2. This was compliant with the bioinformatics standards
in this area. The portal itself was Shibboleth protected. Thus when the
user from the VOTES portal wished to access and use the GEMEPS portal,
they could simply redirect their browser to the GEMEPS portal. Access to
and usage of this portal and the services that it makes available are done
without the need for further reauthentication—one of the key characteris-
tics identii ed for users: “single sign-on.” Figure 12.2 (left) shows a user
searching for experiments containing information on homosapiens -related
microarray experiments conducted on the GPL570 platform targeting the
specii c condition cancer with standard Affymetrix procedures used for
hybridization. The resultant experiments that have been conducted and
are available to that user are shown on the right of Figure 12.2. We note
that this is just one example of a query that can be supported.
As well as querying over metadata of experiments, GEMEPS developed
services that allowed quantii cation of the similarity of experiments them-
selves through comparison of the gene expression levels across experi-
ments. Different statistical similarity models were used for this purpose
and are described in [33].
Assuming that a researcher has identii ed a set of genes that they believe
play a role in cancer for patients identii ed through the VOTES portal, they
may often want to understand the protein and nucleotide sequences asso-
ciated with those genes to compare how similar/dissimilar they are. The
bioinformatics application Basic Local Alignment Search Tool (BLAST) [34]

FIGURE 12.2 GEMEPS showing cancer microarray experiment query.