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).
At the Institute of Zoology and the Institute of Ecology at the
University of
Innsbruck molecular studies play a crucial role in scientific
work. Common aim of our
cooperation is the usage of grid infrastructure for molecular
biology applications:
We want to 1) apply BLAST software (Altschul et al, Basic Local
Alignment Search
Tool, J. Mol. Biol. 215:403-410 (1990)) and 2) introduce software
for the
reconstruction of phylogenetic trees.
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
The usage of the EGEE grid infrastructure for biological
applications will ease the
usage of molecular data. 1) BLAST software allows a rapid
sequence comparison and
directly approximates local similarity. Regularly large scale
comparisons will
facilitate finding genes of interest in the vast number of – for
instance - EST
sequences (expressed sequence tag). 2) Molecular sequence data
can be reconstructed
by use of statistical analyses like maximum likelihood or pair
wise maximum
likelihood distances. Depending on the number and the length of
amino acid sequences
this reconstruction demands enormous computing power.
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)
As molecular biology is very fast evolving the demand of high
throughput computing
will increase in the next years. The more molecular sequences are
known the more
detailed analyses can be taken but the more time and computing
power will be
demanded. Therefore it is necessary for molecular biology groups
to have access to a
grid infrastructure to be able to perform statistical analyses
and phylogenetic
reconstructions.
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.
We tested WU-BLAST 2.0 (Washington University BLAST) with larger
numbers of sequences
on AustrianGrid infrastructure and plan to run WU-BLAST 2.0 with
large databases on
the EGEE grid.
Concerning reconstruction of phylogenetic trees two applications
are now tested and
prepared for use on grid infrastructure: TREE-PUZZLE 5.2 and
software of the ARB
project (Technical University Munich, Germany). Both routines can
handle large data
sets of molecular sequences.
