Transcript Biomed_community_meeting_VB

Enabling Grids for E-sciencE
Biomed community meeting
V. Breton , CNRS
www.eu-egee.org
EGEE-II INFSO-RI-031688
EGEE08 conference, Istambul
Tuesday morning session
Enabling Grids for E-sciencE
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•
•
•
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Introduction (VB)
Results of survey of the life sciences community (VB)
Biomedical grid summer school (L. Milanesi)
EGI (Diana Cresti)
Perspective on EGI from life sciences (VB)
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Other sessions
Enabling Grids for E-sciencE
• Tuesday afternoon: bioinformatics
– Christophe Blanchet
• Thursday morning: medical imaging and drug
discovery
– Johan Montagnat
• Please make sure you upload your slides for these
sessions on the conference programme
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Life sciences cluster
Enabling Grids for E-sciencE
Partner name
Country
Person-Months
ASGC
Taïwan
24
CNR-ITB
Italy
18
CNRS
France
90
CNU
Korea
84
KISTI
Korea
39
UPV
Spain
18
TOTAL
EGEE-II INFSO-RI-031688
273 PM
EGE08 conference, Istambul
Status of cluster activities
Enabling Grids for E-sciencE
• Support for selected services
– AMGA (KISTI, UPV)
– Moteur (CNRS)
• Preparation of the migration to EGI in the life sciences
sector
– See D. Cresti talk
• Support to application porting
– Bioinformatics
– Medical imaging
– Drug discovery
• Cluster management
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Meeting with VPH NoE
Enabling Grids for E-sciencE
• VPH = Virtual Physiological Human
– Initiative supported by EC (first call in 2008, second call in 2009)
– EGEE, supporting project of VPH NoE
• Meeting at UCL with P. Coveney’s group
– V. Bloch, V.B., J. Salzemann, D. Sarramia (LPC Clermont-Fd)
– UCL plays a leading role in VPH NoE WP3
 Design of a toolkit to access grid resources
• Discussions on possible collaboration between VPH
NoE and EGEE
–
–
–
–
Use of the biomed VO
Integration of a cluster on the biomed VO
Sharing of web services to access EGEE resources
Deployment of one VPH use case on EGEE
• Next meeting this Thursday with H. Benoit-Cattin, P.
Coveney, B. Jones and G. Sipos
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Analysis of the needs of the French
life sciences community
Enabling Grids for E-sciencE
•
•
Goal: participate to a multidisciplinary prospective for the national grid initiative
Format: survey circulated in April and May 2008
– 12 questions
– Available online at
http://www.surveymonkey.com/s.aspx?sm=vuEQtHfQu_2fPs1UUyO2aWkQ_3d_3d
•
Very positive community feedback
– Over 400 responses
– More than 60 laboratories in 24 cities
Scientific disciplines represented in the responses
26
20
132
48
205
34
17
10
29
99
61
Agronomie
Biologie cellulaire
Bioinformatique
Biologie évolutive
Biologie moléculaire
Biologie structurale
Chimioinformatique
Drug design
Ecologie, biodiversité
Génomique
Protéomique
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Survey results (I/IV)
Enabling Grids for E-sciencE
Connaissance
personnelleon
desgrids
grilles
Personal
knowledge
80,0%
70,0%
60,0%
Tous
Biologie
50,0%
Santé
40,0%
30,0%
Chimioinformatique
Imagerie médicale
20,0%
10,0%
0,0%
Professionnels de santé
None
Nulle
Limited
Faible
Satisfactory
Satisfaisante
Broad
Etendue
Utilisation
des grilles
dans
les laboratoires
Use
of grids
in the
laboratories
60,0%
50,0%
Tous
40,0%
Biologie
Santé
30,0%
Chimioinformatique
20,0%
Imagerie médicale
10,0%
Professionnels de santé
0,0%
None
Inexistante
EGEE-II INFSO-RI-031688
Limited
Anecdotique
Growing
Croissante
routinely
Courante
EGE08 conference, Istambul
Survey results (II/IV)
Enabling Grids for E-sciencE
Besoins propres sur supercalculateurs
Personal need of
supercomputer resources
Tous
60,0%
Biologie
50,0%
40,0%
Santé
30,0%
Chimioinformatique
20,0%
Imagerie médicale
10,0%
0,0%
Professionnels de
santé
Ne sais pasFaible ou nul
Peu
Importante
Trés
Unknown(<1GFlop)
Small Limited
Significant
Large
importante
(entre
importante
<1GFlop [1-10GF]
[10G-1TF]
>1TFlop
(entre 1 et 10GFlop
et 1 (>
1 TFlop)
10 GFlop)
TFlop)
Besoins
propres sur
clusters
ou grilles
Personal need
of cluster
or grid
resources
60,0%
50,0%
40,0%
30,0%
20,0%
10,0%
0,0%
Tous
Biologie
Santé
Chimioinformatique
Imagerie médicale
Faible ou
Peu
Important
Trés
Professionnels de santé
nul (<10
important
(entre
1 an important
Unknown
Small
Limited
Significant
Large
jours CPU) [10-365CPUdays]
(entre 10 et et
10 ans
(>10
ans
<10CPUdays
[1-10CPUyears]
>10CPUyears
1 an CPU)
CPU)
CPU)
Ne sais pas
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Survey results (III/IV)
Enabling Grids for E-sciencE
Planification des besoins de calculs
50
40
30
20
10
0
très
stables
cours de
Very
stableauduring
thel'année
year
Very
par
pic unstable with peaks
Chemoinformatics
ue
Health
at
iq
Sa
nt
é
Ch
i
m
io
in
Bi
Easy àtoplanifier
plan weeks
in advance
faciles
plusieurs
semaines à l'avance
Hard toà plan
difficiles
planifier
fo
rm
Biology
ol
og
ie
All
To
us
% des réponses
Planning of computing needs
60
50
40
30
20
10
0
très
stables
auduring
cours de
Very
stable
thel'année
year
Very
par
pic unstable with peaks
ue
Chemoinformatics
at
iq
Easyàtoplanifier
plan weeks
in advance
faciles
plusieurs
semaines à l'avance
Hard toà plan
difficiles
planifier
Ch
i
m
io
in
Bi
ol
og
ie
Health
fo
rm
Biology
To
us
All
Sa
nt
é
% des réponses
Planification
de needs
stockage
Planningdes
of besoins
storage
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Survey results (IV/IV)
Enabling Grids for E-sciencE
Interface d'utilisation des ressources informatiques
User interface to grid resources
100,0%
80,0%
60,0%
40,0%
20,0%
0,0%
par
lignes de commande
Command
lines
Tous
Biologie
Santé
via un
portail
web
Web
portal
Chimioinformatique
Imagerie médicale
viadedicated
des applications
métiers
interfaces
Professionnels de santé
70
60
50
40
30
20
10
0
pas de contrainte de sécurité
No constraints
contrôle d'accès
Access control
ue
Chemoinformatics
cryptage
at
iq
Encryption
anonymisation
(pour les
Anonymization
données médicales)
Ch
i
m
io
in
Bi
ol
og
ie
Health
fo
rm
Biology
To
us
All
Sa
nt
é
% des réponses
Sécuritéon
desthe
données
en entrée
Security
input
and output data
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Conclusions
Enabling Grids for E-sciencE
• The life sciences community has homogeneous needs
– Except for security, all sub-communities have very comparable
answers
• The life sciences community needs to access both
cluster grids and supercomputers
– Comparable needs expressed for both infrastructures
– on demand computing: significant fraction of the computing needs
are difficult to plan in advance
• Significant adoption of grids by the research community
– To be counterweighted by the targeted audience
• Security
– 90% of the applications in biology require only access control
– Only 50% for health applications, the other 50% requiring medical
data anonymization
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
EGI: specific thoughts for the life
science SSC
Enabling Grids for E-sciencE
• Adoption of the grid infrastructures is still in its infancy
– It is critical that the biomed VO is continuously operated for the
pioneers already using the grid
• The life science community is very heterogeneous
– Many sub-communities with similar requirements (see survey)
– About 8 ESFRI design studies are related to life sciences




BBSRC: biobanking
ELIXIR: molecular biology
LIFEWATCH: biodiversity
…
– Need to properly interface them to EGI
Life sciences proposed as guinea pigs of the EGI (with particle physics)
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Comments on science gateways
Enabling Grids for E-sciencE
• Development of international gateways is the duty of
the research communities using it.
– Interest/necessity to share some tools (workflow engines) and
technologies (web services, semantic annotation).
• SSC should coordinate the development of science
gateways to guarantee interoperability and integration
• SSC should be in charge of the science gateway to the
biomed VO
– template for the other gateways
– Development started very early in the project to be able to
distribute it to the communities
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul
Questions
Enabling Grids for E-sciencE
• How should the biomed community get organized?
– Should there be one life sciences SSC or one per ESFRI?
– If any, should biomed SSC be funded by EGI, the NGIs or the
community?
EGEE-II INFSO-RI-031688
EGE08 conference, Istambul