EGEE (EU IST-2003-508833 project) – Networking Activities 4: biomedical applications

NA4 biomed status report
Johan Montagnat

AWG face to face meeting

CERN, October 13, 2004

Staff

Hiring completed (as of September 9th)

5 funded project engineers

2 in Spain (UPV Valencia, CNB Madrid)

3 in France (IBCP Lyon, LPC Clermont, CREATIS Lyon)

23 persons registered in the VO from 15 laboratories (3 countries)

mainly application developers

end-users (physicians, biologists...) weakly represented yet

disseminated and loosely coupled community

AWG representatives: Johan Montagnat, Ignacio Blanquer

PTF representatives: Johan Montagnat, Christophe Blanchet

MWSG representative: Christophe Blanchet

Task Force leader: Christophe Blanchet

VO manager: Yannick Legré

Activities

Task (from technical annex)

"Once the applications are selected, the proposing institutes will be invited to carry on with their deployment on the EGEE infrastructure. A significant fraction of the resources allocated to this activity will be devoted to supporting the migration of these new applications”

Strong pressure to get large scale biomedical applications running

Borderline regarding the initial goals of biomed

Suddenly happened in September

Convincing a large user community is a long run process that involves setting up a high quality service first

Focus of project engineers

Strong emphasize on LCG2 deployment until September (contribute and use resources moto)

Strong emphasize on applications development from then

Train a technical team

LCG2/glite experts able to port apps/to help in apps gridification

Applications

Applications description page

http://egee-na4.ct.infn.it/biomed/applications.html

Pilots

GATE – therapy assistance

GPS@ – bioinformatics

CDSS – diagnosis assistance

Internal

SiMRI3D – magnetic resonance image production

gPTM3D – interactive segmentation of medical images

xmipp_MLrefine – alignment of electron microscopy images

External

Mammogrid – diagnosis assistance in breast cancer

Resources

LDAP server at CC-IN2P3

vo-biome.in2p3.fr:389/636 (with ssl), Base DN: o=biomedical,dc=lcg,dc=org

Resource Broker

Production: CNAF (egee-rb-01.cnaf.infn.it), IFAE (lcgrb02.ifae.es)

Test and backup: UPV (xperseo.dsic.upv.es)

RLS

Production: CC-IN2P3 (under configuration and testing)

Temporary: CNAF (datatag2.cnaf.infn.it)

5 UI: LPC, CC-IN2P3, UPV, IBCP (GPS@ portal), CNB

8 CE: LPC (2), CC-IN2P3, CGG, UPV, CNB, SCAI, LAL

334 WN

LPC (72), LPC (50), CGG (4), UPV (10), CNB (8), SCAI (14), LAL (10)

0.9 TB SE (+10 TB coming soon)

LPC (2), CC-IN2P3 (1), CGG (1), UPV (1), CNB (1), SCAI (2), LAL (1)

Still missing services

MPI enable nodes accessible to the biomed VO

CNAF announced availability within the week

Short queues for short jobs (penalizing for several apps)

Latency induced by the resource broker (difficult point)

Having dedicated resources to process short jobs (installation problem)

Service certificate

Authentification of a service giving an anonymous user the ability to run a restricted number of jobs on behalf of the service

Not a problem anymore? Accepted policy in several US CAs.

Stable RLS service

It seems that HEP is experiencing problems with the RLS service too

Interactivity handling

Firewalls are often preventing connection between WNs and the UI.

Fine grain security

File access control. Encryption. Anonymization.

Will soon become critical to enlarge the community of medical users.

Future work planning

Demonstrations development for review

User community enlargement

NA4-SA1 communication

Need for SA1 contact to solve application deployment problems

Need for SA1 information on maintainance operations

NA4-SA1 joint group (first meeting tomorrow)

Privileged contact with French and Spanish rocks

NA4-SA1 joint group mandate

Define the VOs associated with new application community (number and internal structure)

Assist in negotiations for resources for new application area

Ensure ROC/CIC services available to new area – eg. Operational and user support

Ongoing brokerage for resources for application Vos

Ongoing review of community satisfaction and development

Encourage provision of test facilities by resource centres for prospective new application areas

Demonstrations

The Hague, November 22-26

gPTM3D

CDSS

GPS@

What is the demonstrations agenda?

EGEE review

GPS@ as the primary demonstration (genomics, largest user community)

CDSS as a fallback (diagnosis assistance)

or both!?

gLite demonstration?

UPV has developed a volume rendering application (based on the virtual human dataset) on gLite

Biomed task force

Objectives

prepare for the review

application oriented support

Leadership

Christophe Blanchet

Members

5 project engineers

1 SA1 correspondant per application developer (TBC tomorrow)

Actions

applications plan with steps and milestones

meeting and deviations tracking

training (on LCG2)

First demonstrations roadmap

CDSS

October: packaging (RPMs) and deployment on 3 sites (UPV, CNB, LPC).

November: consolidation (first scenario and deployment at CC-IN2P3).

Until review: add more services (search engines) and clinical usecases.

GPS@

October: use RLS to distribute replicate biomed databases on several SE. Test GFAL for accessing registered data.

The Hague: test short queues CEs (performance). Demonstration scenario. Deploy on 5 sites with 5 to 10 CPUs each (CNB, UPV, CC-IN2P3...).

December: Improve results visualization. Make some scale testing.

Until review: Test compound jobs. Add processing algorithms.

gPTM3D

will be finalized next week.

The Hague: require 20 CPUs.

Later: widespread the applications in hospitals (where the non-gridified version is already available).

Tasks assignment

Vincent Lefort (IBCP)

GPS@ porting and deployment on LCG2

The Hague demo / EU review

Christophe Pera (CREATIS)

gLite testing, user reports

biomedical data management middleware

Yannick Legré (LPC)

Biomed VO administration

NA4-SA1 joint group leader (with F. Harris)

VO organisation issues (VOMS...)

Resources and requirements gathering

Angel Merino (CNB)

bioinformatics applications development on LCG2

LCG2 quantitative testing (report on apps testing and updates)

Ignacio Blanquer (UPV)

CDSS deployment on LCG2, work on attracting more users

gLite testing

Other works in progress

Write Once Read Many

Analysis of WORM model completed.

VOMS

study of VOMS current capabilities and gLite integration

Security of biomedical data

encryption and anonimization

medical metadata

Next meetings

Task force next face to face meeting and training

November 3-5, at CERN

Conflict with LCG2 activity, date to change

The Hague meeting

Task force

Biomed

Biomed meeting in Sophia Antipolis

January

Participation to ARDA

October 20-22

EGEE NA4 biomedical applications

Fab

2003-07-22T15:09:39