Speaker
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 demo will show how, through the use of grid resources, the problem of
studying the structural properties of a huge number of protein sequences can
be tackled. Through the use of a parametric job submission procedure, the user
can submit multiple structure prediction jobs and perform a large number of
predictions in a reasonable time frame. This is essential when dealing with a
library made up of 10^5 10^7 protein sequences. In fact, the size of the library
is essential to derive general rules that allow us to pinpoint the particular
properties of natural proteins that make them unique.
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.
The demo will show how the application and related services for job submission
and retrieval of the output have been integrated within the GENIUS portal. In
addition it will be also demonstrated how a non grid trained user can submit
jobs, retrieve the output and obtain a graphical representation of the output
also through the use of molecular graphics plugins. This is a critical point when
dealing with the biology and biomedical community as proper informatics
training is still scarce in these disciplines, while the use of informatics tools in
general and of the grid infrastructure in particular is of unvaluable help in the
research in these fields.
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).
In nature there exists only a tiny fraction of all the theoretically possible protein
sequences. It is thus of interest for the biologists to study the properties of
proteins not present in nature as a way to improve our knowledge on the
unique properties of the existing protein sequences. The demo will deal with
the use of the protein structure prediction software Rosetta in a grid
enviornment as a tool to study the structural properties of large protein
sequence libraries.
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)
The demo presentation will also deal with aspects that still need
development/improvement. In particular, a simplified, web-based access to the
grid infrastructure allows easy and fast submission of jobs and further
developments along this path are critical for the access of novel communities to
the grid resources.
