Speaker
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 the efficiency of the grid-enabled docking service has been
demonstrated by the data challenge, we expect a well
customized interface can encourage biology researchers to use the
service for their daily research. In developing the
web interface, we experienced that adopting high-level Grid
application frameworks (e.g. DIANE and GANGA) can
dramatically reduce the effort in handling Grid jobs, concerning
the work of failure recovery, and of application
specific monitoring and bookkeeping.
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 avian flu data challenge in last spring has successfully
demonstrated a high-througput docking service on
the EGEE infrastructure. The next step is to make this service
more accessible to real biology end-users rather than
grid specialists. Collaborating with biomedical researchers, we
have developed an intuitive web interface for biologists
to access the massive molecular docking service on the EGEE
infrastructure.
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.
This work is built on top of the DIANE framework. DIANE was
originally developed for handling the distributed
applications within a Master-Worker model. It provides an overlay
system on top of the Grid system, in which the
pull-mode scheduling and failure recovery mechanisms are
implemented based on the CORBA protocol. On the other
hand, the DIANE framework hides the details of the job operations
on the Grid so that application developers can
concentrate on the implementation of application logic and
interface design. DIANE interfaces the EGEE
infrastructure through a high-level grid tool, GANGA
(http://cern.ch/ganga).
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
Aiming at making the grid-enabled docking service more useful for
biologists, we developed a web-based user
interface on top of the DIANE framework (http://cern.ch/diane),
trying to reduce researchers’ effort in accessing the
service and in analyzing the docking results. By hiding the
technical details, the interface exposes only the
configurations meaningful for biologists. Through this interface,
biologists could set a filter on a compound library
and select interesting targets and ligands by visually examining
their structures. Leveraging on the interactive
feedback feature of the DIANE framework, results of finished
dockings are not only ranked in table; they are also
transformed into 3-D structures so that biologists can
immediately look into the docking poses and download
corresponding results to their local disk for further analysis.
