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

Overview of biomedical work
Johan Montagnat

NA4 open meeting

Catania, July 15, 2004

Status

Quick-off meeting in Cork, April 18th

set up executive and technical structures

pilot applications identification

external application integration procedure

Web

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

project-eu-egee-na4-biomed-applications@cern.ch

Human resources

4FTE became 5 (LPC + CREATIS = LPC + CREATIS + IBCP)

CNB, Madrid: Angel Merino

UPV, Valencia: 4 * 0.25 FTE coordinated by Ignacio Blanquer

LPC, Clermont-Ferrand: Yannick Legré

CREATIS, Lyon: one candidate, starting September 1st

IBCP, Lyon: one candidate to hire very soon

Organisation

VO management

internal VO management (Y. Legré)

biomed VO hosted at CC-IN2P3

Technical team

middleware expertise

testing internal to biomed applications

Participation to other groups

Application Working Group (I. Blanquer, J. Montagnat)

Project Technical Forum (C. Blanchet, J. Montagnat)

Middleware Security Group (C. Blanchet)

Data management (J. Montagnat)

Web

Webmaster: Y. Legré

Detailed meetings minutes

Technical team

Role

Group of technical people (acquiring and) providing expertise, at the interface between middleware developers and users

Contact

project-eu-egee-na4-biomed-twg@cern.ch

Composition

5 funded engineers

2 test team representatives

8 unfunded participants

First objectives

Test middleware

Acquire expertise

Provide feedback

Work plan followed

Meetings

biomed plenary: Cork (April), Lyon (June), Catania (July), Madrid (October)

AWG (phone, weekly)

MWSG: CERN (May, June), Stockholm (August)

PTF: CERN (June)

JRA1: CERN (June)

ARDA: CERN (June)

JRA2: phone (June)

BIRN: CERN (June)

Participation to NA4 tasks and deliverable

TNA4.1: biomedical requirements

DNA4.1: applications interface

Testing and training

Access to LCG2

LCG2 deployment

Pilot applications deployment

Access to glite

TNA4.1: Requirements

http://egee-na4.ct.infn.it/requirements/

Critical for development

mid-term requirement

long-term requirement

1. Large user community

anonymous/group login

multiple VOs/subgroups

2. Data management

application metadata

data updates and data versioning

3. Security

application data filtering

disk / network encryption

4. Limited response time

fast queues for short jobs

high priority jobs/privileged users

6. Interactivity

communication between user interface and WNs

7. Parallelization

MPI site-wide

8. Pipeline processing

pipeline description language / scheduling

9. Network

outbound connectivity

10. Development

C++/Java APIs

DNA4.1: application interfaces

GENIUS: generic portal

Interface to middleware services

exposition to middleware

required services

Interface level

Application Programing Interfaces!

from APIs to service APIs

Common application services

and middleware services

Integrated applications

web	application

interface specific interface

Prototype and

testing applications

Service aware

applications

Grid

jobs

WSRF

CLI

web portal

API

WN API

WSRF

Progress report

Deploy applications and testing

Access to infrastructure

Pilot applications for early testing

Internal applications

Identify health-related applications

External application integration procedure

Mammogrid

Other contacts (Geneva hospitals, Phylogeny BBE, Gene expression MPBA)

Deploy biomed resources

Hardware resources

LCG2 deployment

Access to infrastructure

LCG2 infrastructure

First “Hello biomed world” job executed on June 23

VO hosting and User Interface at CC-IN2P3

VO acceptance at CNAF

Lot of difficulties related to VO:

Adding new VOs in LCG2 (tedious manual configuration, LCFG overwritting new VOs every night...)

VO acceptance (political level)

VO acceptance (technical level: RB, resources...)

Jobs submitted from a biomed UI at IBCP

RC to be hosted at CC-IN2P3

glite prototype

First glite job executed on June 17

Few testing done today, focus on LCG2

Low expertise level

Pilot applications report

CDSS: Clinical Decision Support System (UPV)

Application that Extracts Medically Relevant Knowledge from a Large Set of Information with the Objective of Guiding the Practitioners in their Clinical Practice.

Trained Databases Available

Classification of Tumours of Soft Tissues

Diagnostic and Classification of Thalassemia and Other Anaemia

Bioinformatics: Study of the Human Genome

Migration to LCG2

CDSS ported on LCG2 (UPV installation)

To high job pay-off

Service oriented architecture

Redesign needed for taking into account the batch-oriented nature of LCG2

Pilot applications report

The Web

LCG GRID

WN

CE

UI

WN

CE

UI

WN

CE

UI

Replica

Manager

SE

UI

Resource

Broker

User

Interface

Web

Server

Java

Web

Start

Web

Browser

Https + User Certificate

Request.xml

Https

Reports.xml

Pilot applications report

GPS@: genomics web portal (IBCP)

Already ported on EDG through an application C++ API

http://gpsa.ibcp.fr/

Adaptation to LCG2 middleware in progress

Application API migration

XML description of bioinformatic jobs

Need last RedHat distribution for the web portal

service certificate needed

Tested on LCG2 for 4 algorithms (PattInProt, secondary structures prediction)

Pilot applications report

GATE: radiotherapy planning (LPC)

Demonstrated at the last EDG review

Ported to LCG2

Deployment

On CC-IN2P3

On Clermont-Ferrand site

Medical

records

Image binaire

Size 19M

DICOM

CT slices

DB

User interface

Anonymisation

Assembling

SE

Computing center

SE

Computing center

CC-IN2P3

CLERMONG

application reports

SIMRI: parallel MRI simulator (CREATIS)

migration to MPICH-G2

on-going tests at CC-IN2P3

no parallel jobs on LCG2

on-going test at CINES (supercomputing center)

g-PTM3D: interactive radiological images processing (LAL)

radiological images manipulation

interaction and jobs execution

LCG2 pay off compensated by internal scheduler

interaction through bypass unsatisfying (std input/output used for communication, far too slow)

Mammogrid

developed on AliEN

to be ported on glite

Biomed resources

Material resources deployed

Clermont-Ferrand: > 100 nodes, waiting (?) for LCG2 certification

UPV: 3 AMD/Pentium PCs for LCG2 services, 20 processor cluster running RH7.1

IBCP: 10 PCs dedicated to LCG2

CREATIS: up to 8 PCs available

CNB: 20 processors

Software deployed

Clermont-Ferrand: UI, CE, SE, WNs, GENIUS web portal

UPV: RB, MDS, BDII, UI, CE, SE, WNs

IBCP: UI, CE, SE, WNs, 1 web portal

CREATIS: problems encountered installing multiple services on PCs

CNB: UI, CE, SE, WNs, hardware compatibility problems with RH7.3

Storage Resource Broker (SRB) testing

Production stable at CC-IN2P3

Evaluation at Clermont-Ferrand and I3S

Conclusions

Work done

Ready to go on LCG2

Pilots ported to LCG2

Applications emerging

Contributions to NA4 general activities

Main problem encountered and weaknesses

Late access to LCG2, low level of expertise

Weight of LCG2 deployment

Weak response from e-health EU projects

Loose integration of biomedical community – external evaluation mentioned it as one of the few risk factor

Future and roadmap

Infrastructure testing on-going

Applications porting on-going

Mammogrid integration on glite

Demonstration for the first project review (GPS@?)

EGEE NA4 biomedical applications

Fab

2003-07-22T15:09:39