Speaker
Describe the scientific/technical community and the scientific/technical activity using (planning to use) the EGEE infrastructure. A high-level description is needed (neither a detailed specialist report nor a list of references).
Microarray experiments permit a genome-scale evaluation of gene
functions
and are therefore among the most topical and prominent
developments of
biomedical research. Our target user group includes: Doctor,
researchers,
biologists, bioinformatics specialists carrying out DNA
microarray experiments.
Report on the experience (or the proposed activity). It would be very important to mention key services which are essential for the success of your activity on the EGEE infrastructure.
Bioinformatics applications in general and microarray experiments
in particular
are perfectly tailored to Grid infrastructures. Motivated by this
fact, University of
the Aegean proposed to ‘Gridify’ a selected number of microarray
analysis and
normalization applications. These applications focus on cDNA
arrays. The target
Grid infrastructure was the Hellas Grid portion of the
pan-European Grid
infrastructure developed for e-science in the scope of the EGEE
(Enabling Grids
for E-Science in Europe) project and its successors. The idea was
proposed in
the scope of the Grid-App tender issued by the Greek General
Secretariat of
Research and Technology (GSRT) and was warmly embraced by the
evaluators.
The application will leverage a host of Hellas Grid (i.e. gLite)
middleware
middleware services inlcuding security, information services,
data management,
job submission, and resource management . The paper elaborates
on the use
of these services based on our experiences.
Describe the added value of the Grid for the scientific/technical activity you (plan to) do on the Grid. This should include the scale of the activity and of the potential user community and the relevance for other scientific or business applications
Economic parameters are a major obstacle to microarray
experiments, since
some processes are extremely computationally demanding. This is
particularly
true for the normalization process, which deals with the fact
that every repeat
experiment will give rise to a certain amount of variations.
Variations can be
minimized based on statistical methods, which in turn allows one
to compare
the expression levels between multiple microarray experiments.
Normalisation
procedures rely on the fact that gene expression data can follow
a normal
distribution. Thus the entire distribution can be transformed
about the
population mean and median without affecting the standard
deviation. cDNA
arrays can contain up to 25,000 gene-complementary seqsequences
while high-
density oligonucleotide arrays can hold more than 100,000 proceses.
Grid computing can accelerate the computations associated with
microarray
normalization, while at the same time providing access to vast
amounts of
federated storage.
With a forward look to future evolution, discuss the issues you have encountered (or that you expect) in using the EGEE infrastructure. Wherever possible, point out the experience limitations (both in terms of existing services or missing functionality)
Our recently started developments involve the following steps:
I)Transforming our microarray applications (from MATLAB, which is
not currently
supported on HellasGrid.) to supported executables such as the
open-source
GNU Octave (forge) .
II)Exploiting appropriate gLite middleware components in the
areas of security
(GIS), information services (R-GMA), data management (LFC), job
submission
(WMS), and resource management.
III) Implementing an access portal based on UI images available.
