Speakers
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
As the protein folding simulation is a compute intensive task and
the number of
interesting molecules may be in the order of millions, therefore
a usage of the Grid
infrastructure comes as a natural solution for providing
computing power. The storage
requirements of the application are not negligible as well, and
may reach an order of
terabytes. In addition to raw computing power offered by the
Grid, the collaboration
aspect becomes important as well. Since there are many research
groups developing
various computational models and producing their simulation data,
making them
available on the Grid enables collaborative work on model
verification and testing.
In our project results obtained using two methods (one using a
standard Rostetta tool
and other using a newly developed model by JUMC team from Krakow)
and leading to
similar structure of protein are going to be synthesized and
examined experimentally
by another team.
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)
When developing scientific experiments, which are applications
using the Grid from
the client-side, there is a problem of lacking or insufficient
standard client API to
the underlying middleware. It should be possible to have a
lightweight and easy to
install client library for EGEE in all important programming
languages. Currently
available solutions are discouraging the developers of scientific
applications from
integrating with and from using the EGEE software in their
experiments.
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).
The contemporary pharmacology facing the problem of the
individual therapy design,
requires the understanding of the activity of molecules (such as
proteins). in the
case of
proteins the activity is implied by the 3-dimensional structure,
therefore the
simulation of the folding process is crucial in the research. In
the scope of
EUChinaGRID project the large number of "never born proteins" of
70 amino acids in
polypeptide chain is planned to be predicted using 2 methods.
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.
Our application requires simulating of miilions of proteins using
our software,
therefore the first challenge was to grid-enable the application.
This task was
accomplished by preparing a self-contained package of the
software which could be
deployed and run as a grid job with minimal requirements. For
storing the results the
grid storage is used and all resulting files are registered using
grid catalogues
(namely LFC). Another challenge was the management of such a
large experiment and for
that purpose the database system integrated with a portal and
with automating job
submission system has been developed. The portal is based on
Gridsphere framework and
uses GridwiseTech LCG_API to interface with the EGEE middleware.
The portal may be
used for the user-friendly definition of experiments and is
integrated with the
scientific visualization and analysis tools.
