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
GPS@ Web portal and gBIO-WS make the remote access and bioinformatics job submission
easier on the grid. We have used, as testcase, the ClustalW multiple alignment tool
run on a remote Grid platform, to analyze the variability of a subset of sequences.
Biologists can submit bioinformatics jobs on the Grid by using their usual Web
client, but also integrate these grid services within complex workflow combining
different databases and tools. They, then, benefit from the large-scale computing
resources of the Grid, from their usual and local working environment. Grid computing
and storage facilities will also permit GPS@ and gBIO services to scale to thousands
of daily user as much as aligning complete genomes or proteomes. In this testcase, we
consider a common task for bioinformaticians working on Hepatitis C Virus: doing a
multiple alignment of sequences issued from different strains, where user is
uploading its own sequence databank of HCV sequences.
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 have put online two multiple alignments Web Services on the CNRS IBCP servers. One
is accessible through a classical Web interface, the other one can be used through a
SOAP client such as Taverna or Triana, but also a user one built with gSOAP, perl
SOAP::Lite or Java. These Web services can process the submitted alignment on two
different computing environments: a local cluster, and the grid platform of the
EU-EGEE project. The GPS@ sub-process that have submitted the job, is monitoring the
job with trhe EGEE commands. When achieved, the GPS@ automat downloads the result
file containing the multiple alignment computed by ClustalW, and processed it in a
HTML page showing, in a colored and graphical way, the list of aligned protein
sequences. This is directly inherited from the original NPS@ portal, providing
biologists with a well-known interface and way of displaying results.
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).
Bioinformatics analysis of data produced by high-throughput biology, for instance
genome projects, is one of the major challenges for the next years. Some of the
requirements of this analysis are to access up-to-date databanks and relevant
algorithms. Since 1998, we are developing the Network Protein Sequence Analysis
(NPS@) Web server , that provides the biologist with some most common resources for
protein sequence analysis, integrated into several pre-defined and connected workflows.
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)
Future works will be done about applying this Grid WebServices interface to other
programs. We will, for example, work to put online, as Web Services, a selected panel
of other protein alignment methods, but also similarity searching programs, like
BLAST or SSEARCH, raising the issues of large and numerous databases management in
Grid environment.
