Life Sciences

Pilot applications in the life sciences area have been included in the EGEE project since the beginning. About twenty regularly used applications are now available and several new initiatives are currently being investigated.

The biomedical applications area is a broad scientific field which has been divided in three different sectors in EGEE-II. Each activity sector has earlier demonstrated a significant usage of the grid infrastructure. The medical imaging sector targets the computerized analysis of digital medical images. It includes medical data federation, compute-intensive medical procedures, large data sets processing and statistical studies over large populations. The bioinformatics sector targets gene sequences analysis. It includes genomics, proteomics and phylogeny. The drug discovery sector aims to help speed up the process of finding new drugs through in silico simulations of proteins structures and dynamics.

EGEE to EGI transition

This wiki is also going to be used to steer up discussions and brainstorming for the preparation of the Life Sciences SPecific Support Center.

How to participate?

Depending on your area of interest, you can contact one of the activity sector leader:

• Medical Imaging: Johan Montagnat
• Bioinformatics: Christophe Blanchet
• Drug Discovery: Vincent Breton

New application supporters should first fill in and return the following questionnaire. Once the application has been accepted, the users can obtain an access by following this procedure:

• Obtain a certificate from your CA: find your CA on the EUGridPMA map.
• Register to the biomed VOMS server.
• Install a gLite user interface or create an account on an existing user interface.

More technical information on accessing the grid infrastructure is provided this former page or the GGUS documentation page. Documentation on the gLite grid middleware is available here. For installing a UI, here are some configuration parameters you will need for accessing the biomed VO services:

RB_HOST=boszwijn.nikhef.nl
LB_HOST=boszwijn.nikhef.nl
WMS_HOST=egee-wms-01.cnaf.infn.it
PX_HOST=myproxy.cern.ch
BDII_HOST=lcg-bdii.cern.ch
REG_HOST=lcgic01.gridpp.rl.ac.uk
CA_REPOSITORY="rpm http://linuxsoft.cern.ch/ LCG-CAs/current production"
VO_BIOMED_VOMS_SERVERS="'vomss://voms-biomed.in2p3.fr:8443/voms/biomed?/biomed/'"
VO_BIOMED_VOMSES="'biomed cclcgvomsli01.in2p3.fr 15000 /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=cclcgvomsli01.in2p3.fr biomed'"

Life sciences application sectors

Medical Imaging

Due to the generalization of digital medical images availability, there is a growing demand for archiving, federating and analyzing medical image databases which are geographically distributed over many acquisition sites. The medical imaging sector covers all aspects related to computerized medical images analysis including medical images management, medical images post-processsing, medical images simulation and image-based therapy planning. Grid technologies help addressing data distribution and compute intensive problems such as medical data stores federation, secure data access, large databases concurrent analysis, complex analysis procedures set up and imaging physics simulation.

Medical Imaging resources:

• Examples of applications ported to the EGEE infrastructure
• Medical Data Manager
• MOTEUR workflow manager
• P-GRADE portal interface

• March 2009 meeting in Catania
• September 2008 meeting in Istanbul
• October 2007 meeting in Budapest
• November 2006 meeting at CERN
• September 2006 meeting in Geneva
• July 2006 meeting in Sophia Antipolis

Bioinformatics

• Examples of applications ported to the EGEE infrastructure

Drug Discovery

• Examples of applications ported to the EGEE infrastructure

Biomed VO technical support team

technical support team page

Biomedical application resources

• Internal mailing list : project-eu-egee-na4-ls@cern.ch
• Discussion mailing list: project-eu-egee-life-science-community@cern.ch
• Biomedical application requirements analysis
• Plan of work (DNA4.1)
• VOMS server
• EGEE-II NA4/life sciences web site
• HealthGrid association

-- CharlesLoomis - 22 Jul 2008

• slides_for_Steve_Newhouse.ppt: Slides for Cancer Informatics conference 2009