Transcript presentation_LIA_180708.ppt

France-Korea Particle Physics
Laboratory: an International
Associated Laboratory for escience and particle physics
V. Breton CNRS-IN2P3
Table of content
• What is a LIA ?
• Example: the FKPPL
• Introduction to grids
• Grid-enabled virtual screening: the example of
WISDOM
• Conclusion
July 18th 2008 – V. Breton
International Associated Laboratory –
LIA (1/3)
• An LIA is a "laboratory without walls" and is not a legal
entity.
• It brings together laboratories from CNRS and from one
other country.
• These laboratories contribute human and material
resources to a common, jointly-defined project designed
to "add value" to their individual pursuits.
• An LIA agreement is for 4 years, renewable twice.
July 18th 2008 – V. Breton
LIA(2/3)
• The laboratories comprising an LIA retain their
independence, their regular status, their director and their
separate locations.
– Co-directors of the LIA are appointed if so desired.
• An LIA receives earmarked funding from the CNRS and the
partner institutions, for equipment, scientific missions,
associate research positions, etc.
• It is coordinated by a scientific management committee,
which determines the research program to be submitted to
the steering committee. The latter is composed of
representatives of the two partner institutions as well as
established scientists from outside the LIA.
July 18th 2008 – V. Breton
LIA(3/3)
• When to apply for LIA status?
– Proposals for the creation of an LIA may be filled at any
time with a laboratory's scientific department.
• Who makes the decision to approve an LIA proposal?
– The decision to create an LIA is made by the CNRS and its
foreign partner institution.
• When the proposal has been accepted, an agreement is
established between the Director General of the CNRS
and the supervisory board of the partner institution
July 18th 2008 – V. Breton
A brief history
•
2005
– December: first contacts between François Le Diberder, Do-Won Kim
and Marianne Noël
 François Le Diberder: deputy director of CNRS Institute of Nuclear and
Particle Physics
 Do-Won Kim: professor of physics at Kangnung University
 Marianne Noël: Attache for science and technology at French embassy in
Seoul
•
2007
– April : signature of CNRS – KISTI MoU during the 3rd session of the
Korea-France joint committee for scientific and technological
cooperation
– November : Visit to Korea of Blaise Pascal University president
– December : François le Diberder visit to Korea - addition of new
partners and of a new project on ILC microelectronics
•
2008
– March 20th 2008: signature of the LIA creation document
at the French Embassy in Seoul
July 18th 2008 – V. Breton
Partners
• Korean partners
–
–
–
–
–
–
–
KISTI (Daejeon)
Chonnam National University (Gwangju)
EWHA Womans University (Seoul)
Kangnung National University
Korea Institute of Radiological and Medical Sciences (Seoul)
Pohang Accelerator Laboratory (Seoul)
Sung Kyun Kwan University
• French partners
–
–
–
–
CNRS
Blaise Pascal University (Clermont-Ferrand)
University Paris XI (Orsay)
Ecole Polytechnique (Palaiseau)
July 18th 2008 – V. Breton
FKPPL management
• Steering Committee members
– Professor Dong-Pil Min (Seoul National University), co-chairman
– Professor François Le Diberder (Stanford University), cochairman
– Professor YungE Earm, Seoul National University
– Doctor Jysoo Lee, KISTI
– Doctor Mannque Rho, CEA
– Doctor Jean-Eudes Augustin, CNRS-IN2P3
– Professor Alain Baldit, University Blaise Pascal
– Doctor Dominique Boutigny, CC-IN2P3
• Co-directors
– Doctor O. Byeon, KISTI
– V.B., CNRS-IN2P3
July 18th 2008 – V. Breton
FKPPL scientific projects
•
FKPPL focusses on particle physics and e-science
– Both require international collaboration
– Particle physics is the first user community to have completely adopted the
grid technology
Project name
Coordinators
Partners
Status
ILC calorimeter
Yongmann Yang, EWHA
Jean-Claude Brient, LLR
EWHA Womans Univ., Kangnung Nat.
Univ.,LPC, LLR
Approved
ILC
microelectronics
Jongseo Chai, SKKU
Christophe de la Taille, LAL
Sung Kyun Kwan Univ., Korea Institute of
Radiological and medical Sciencces,
Pohang Accel. Lab. LAL, LLR
Approved
Grid computing
S. Hwang, KISTI
D. Boutigny, CC-IN2P3
KISTI, CC-IN2P3
Approved
WISDOM
Doman Kim, CNU
V. Breton, LPC
Chonnam Nat. Univ., KISTI, Kangnung
Nat. Univ., LPC
Approved
ALICE
Yongwook Baek, KNU
Pascal Dupieux, LPC
Kangnung Nat. Univ. LPC
Submitted
CDF
Kihyeon Cho, KISTI
Aurore Savoy-Navarro, LPNHE
KISTI, LPNHE
Submitted
July 18th 2008 – V. Breton
What is a grid ?
• a fully distributed, dynamically reconfigurable, scalable
and autonomous infrastructure to provide location
independent, pervasive, reliable, secure and efficient
access to a coordinated set of services encapsulating
and virtualizing resources (computing power, storage,
instruments, data, etc.) in order to support problem
solving and knowledge generation across multiple
administrative domains.
July 18th 2008 – V. Breton
The different kinds of grids
Computing Grid
For data crunching applications
•
Computing grids provide resources for intensive calculations
– Particularly intestesting for embarassingly parallel computations (MonteCarlo)
– Currently used for docking and molecular dynamics
•
Data Grids allow distributed and secured storage and access to biochemical data
– Databases (Zinc, PDB)
•
Knowledge grid are about information management
– Goal: allow end users to access all the computing and data resources of
the grids while manipulating concepts they are familiar with
– Requirements: data interoperability and ontologies
Data Grid
Knowledge Grid
Distributed and optimized storage of
large amounts of accessible data
Intelligent use of Data Grid for
knowledge creation and tools
provisions to all users
ICT for Health, ISTAG WG, March 2004
July 18th 2008 – V. Breton
EGEE Grid Infrastructure
Enabling Grids for E-sciencE
Enabling Grids for E-sciencE
Flagship European grid infrastructure project
Now in 3rd phase with more than 100 partners
Size of the infrastructure today:
• > 250 sites in 48 countries
•One in Korea (KISTI)
• > 70 000 CPU cores
• ~ 5 PB disk + tape MSS
• > 150 000 jobs/day
• > 9000 registered users
12
EGEE-II
INFSO-RI-031688
INFSO-RI-508833
V. Breton, July 18th 2008
Scientific Applications on EGEE
Enabling Grids for E-sciencE
• 6 scientific disciplines
are routinely using the
EGEE grid
– >100 applications deployed
6/2006
2/2007 1/2008
Astron. & Astrophysics 2
8
9
Comp. Chemistry
6
27
21
Earth Science
16
16
18
Fusion
2
3
4
High-Energy Physics
9
11
7
Life Sciences
23
39
37
Others
4
14
21
Total
62
118
117
INFSO-RI-508833
Condensed Matter Physics
Comp. Fluid Dynamics
Computer Science/Tools
Civil Protection
V. Breton, July 18th 2008
13
Computational Chemistry
Enabling Grids for E-sciencE
• Becoming the second user of the infrastructure after
High Energy Physics
INFSO-RI-508833
V. Breton, July 18th 2008
14
Computational chemistry on EGEE
Enabling Grids for E-sciencE
• Software deployed on the grid
– Free sofware: GAMESS, COLUMBUS, DL_POLY, RWAVEP or ABCtraj
– Licensed software: Amber, Gaussian, Turbomole and Wien2K
• Contact point: Mariusz Sterzel, CYFRONET, [email protected]
INFSO-RI-508833
V. Breton, July 18th 2008
WISDOM In silico Drug Discovery
Enabling Grids for E-sciencE
Enabling Grids for E-sciencE
• WISDOM: http://wisdom.healthgrid.org/
• Goal: find new drugs for neglected and emerging
diseases
– Neglected diseases lack R&D
– Emerging diseases require very rapid response time
• Need for an optimized environment
– To achieve production in a limited time
– To optimize performances
• Method: grid-enabled virtual docking
– Cheaper than in vitro tests
– Faster than in vitro tests
16
INFSO-RI-508833
V. Breton, July 18th 2008
WISDOM partners
•
Laboratories with expertise in grid technology
– KISTI in Korea
•
“Wet” laboratories for in vitro and in vivo studies
– Chonnam national University
SCAI Fraunhofer:
Knowledge extraction,
Chemoinformatics
LPC Clermont-Ferrand:
Biomedical grid
CEA, Acamba project:
Biological targets,
Chemogenomics
HealthGrid:
Biomedical grid,
Dissemination
Univ. Los Andes:
Biological targets,
Malaria biology
July 18th 2008 – V. Breton
Univ. Modena:
Biological targets,
Molecular Dynamics
ITB CNR:
Bioinformatics,
Molecular modelling
Univ. Pretoria / CSIR:
Bioinformatics, Malaria
biology
Chonnam nat. univ.:
In vitro testing
KISTI:
Grid technology
Academia Sinica:
Grid user interface
Biological targets
In vitro testing
Mahidol Univ.:
Biochemistry, in vitro testing
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High Throughput Virtual Docking
Enabling Grids for E-sciencE
Enabling Grids for E-sciencE
Millions of chemical
compounds available
in laboratories
Chemical compounds : ZINC
Molecular docking : FlexX, Autodock
Targets structures : PDB
Grid infrastructure : EGEE
Chemical compounds :
Chembridge – 500,000
Drug like – 500,000
High Throughput Screening
1-10$/compound, nearly impossible
Molecular docking (FlexX, Autodock)
~80 CPU years, 1 TB data
Computational data challenge
~6 weeks on ~1000/1600 computers
Targets :
Plasmepsin II (1lee, 1lf2, 1lf3)
Plasmepsin IV (1ls5)
Hits screening
using assays
performed on
living cells
Leads
Clinical testing
Drug
18
EGEE-II
INFSO-RI-031688
INFSO-RI-508833
Application to life sciences, J. Montagnat,
June18th
18, 2008
V. Breton, July
18
Virtual screening pipeline
Enabling Grids for E-sciencE
Molecular docking
FLEXX/
AUTODOCK
Molecular dynamics
AMBER
Complex
visualization
CHIMERA
Catalytic aspartic residues
in vitro
WET LABORATORY
in vivo
INFSO-RI-508833
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19
The present WISDOM architecture
Enabling Grids for E-sciencE
Enabling Grids for E-sciencE
Major new features:
- improved data management
- secure storage
- migration to web service
Credit: J. Salzeman, V. Bloch
20
INFSO-RI-508833
Healthgrid … – March
8th, 2007
V. Breton
V. Breton,
July– 18th
2008
20
WISDOM-II: A huge international
effort
Enabling Grids for E-sciencE
Enabling Grids for E-sciencE
Significant contributions from several
International grid infrastructures
Over 420 CPU years in 10 weeks
A record throughput of 100.000 docked compounds per hour
INFSO-RI-508833
Healthgrid … – March
8th, 2007
V. Breton
V. Breton,
July– 18th
2008
21
21
MD refinement using Amber
Enabling Grids for E-sciencE
Best hits from docking
step based on:
• Docking energy
For one complete simulation, all necessary steps are
embedded in one single script.
• Docked pose
Preparatory Phase
Mol2
Antechamber
prepi
Target
+prepi
Re-ranking and Analysis
Phase
Simulation Phase
top, crd
Leap
Sander
Min
top, crd
min.rst
min.rst
Sander
MD
md.rst
top
Ptraj
Output
pdb, top
MMPBSA
Output
Final output appended into a file
A. Ferrari, G. Degliesposti, M. Sgobba, G. Rastelli. Validation of an automated procedure for the prediction of relative free
energies of binding on a set of aldose reductase inhibitors. Bioorganic & Medicinal Chemistry. 2007. In Press.
INFSO-RI-508833
V. Breton, July 18th 2008
Grid Performances for MD
Enabling Grids for E-sciencE
25, 000 compounds:
• Plasmepsin: 5000 compounds
• Pf-DHFR: 15,000 compounds
• Pf-GST: 5000 compounds
Number of Jobs
500
Total Number of compounds
25000
simulated
Estimated duration on 1 CPU
347 days
Duration on the grid
25 days
Maximum number of concurrent
90
running jobs
Number of computing elements used
1
Average duration of a job
16.6
hours
INFSO-RI-508833
V. Breton, July 18th 2008
Virtual screening on the grid:
deployment status
Enabling Grids for E-sciencE
Dates
Target (s)
Summer
Malaria:
2005
plasmepines
Spring 2006
Avian flu:
CPU consumed
Data
EGEE AuverGrid
produced
80 years
1TB
100 years*
800 GB
Neuraminidase N1
Winter 2006
Malaria: GST,
Status
First data
In vitro tests
challenge
In vivo tests
<45 days needed
In vitro tests
for preparation
400 years
1,6TB
DHFR, Tubulin
Fall 2007
Specific features
> 100.000
Analyzed,ready
dockings / hr
for in vitro tests
Under analysis
Avian flu:
Estimated 100 CPU
Estimated
Joint deployment
Neuraminidase N1
years*
800 GB*
on CNGrid
Diabetes:
Estimated 120 CPU
Estimated
New production
amylase
years
800 GB
environment
Summer
Malaria:
To be estimated
To be
Joint deployment
2008
DHPS
estimated
on desktop grid
Spring 2008
INFSO-RI-508833
Under way
In preparation
V. Breton, July 18th 2008
KISTI contribution to WISDOM
Enabling Grids for E-sciencE
• E-science division
– Partner of EGEE-III (European project)
– Contact point: S. Hwang, [email protected]
• Improve data management services on EGEE
• Improvement to the WISDOM production environment
– Allow the use of several biochemical data servers
• Deploy large scale docking computations on amylase
– Collaboration with CNU and LPC Clermont-Ferrand
• DrugScreener-G
– Goal: provide a user-friendly integrated environment for Grid-based
large-scale virtual screening for users without much knowledge of
Grid computing
– Target users: Bioinformaticians, Biologists, Drug Chemists
– Contact point: Jincheol Kim, e-science division, KISTI,
[email protected]
INFSO-RI-508833
V. Breton, July 18th 2008
DrugScreener-G : Architecture
CNU contribution to WISDOM
• Lab. of Functional Carbohydrate Enzyme and Microbial
Genomics, led by Prof. D. Kim ([email protected])
– Partner of EGEE-III (European project)
– Partner of STAR project (Korea-France funding program)
• In vitro test of the best compounds selected in silico on
the grid
– Malaria: 6/30 compounds similar or better than PepstatinA on
plasmepsin target
– Avian flu: 20% of compounds better than Tamiflu on neuraminidase
N1 target
– Best compounds patented in Korea
• Search for new drugs against diabetes
– First target studied: amylase
July 18th 2008 – V. Breton
Summary of the existing
collaborations on grids
• Bilateral agreements
– Memorandum of Understanding between Chonnam Nat. Univ. and
Univ. B. Pascal, Kangnung Nat. Univ. and Univ. B. Pascal
– STAR project( CNU, KNU, CNRS)
– International Associated Laboratory FKPPL (CNU, KISTI, CNRS, Univ.
Blaise Pascal)
• EU project
– KISTI, CNU involved in the EGEE-III project (FP7) with CNRS and
Univ. B. Pascal
 Participation to the Life Sciences cluster of EGEE-III
July 18th 2008 – V. Breton
Conclusion
• The FKPPL LIA offers a framework for collaboration on
particle physics and e-science between Korea and France
– July 14 – 25: Grid school at Seoul National University
 Installation of grid services
 User tutorial
 Advanced tools for data analysis
– July 21 : first FKPPL Steering Committee meeting
• Grids are under adoption by the Computational
Chemistry community
– Popular software like Amber, Gaussian deployed on EGEE grid
– Well fitted for embarrassingly parallel applications (Monte-Carlo)
– Potential limitations:
 Licensing issues
 Memory < 2GB / node
July 18th 2008 – V. Breton
Perspectives
• In France
– French Ministry of Research has organized a wide consultation
for the deployment of a multidisciplinary grid for scientific
production
– Contribution of the Computational Chemistry community is
important
– Contact point: Guy Wormser, director of Institut des Grilles,
[email protected]
• In Korea
– First grid school in Seoul currently going on
– Deployment of grid nodes foreseen in Korean universities
– Contact point: Dr Soonwook Hwang, KISTI, [email protected]
July 18th 2008 – V. Breton
PCSV group at LPC Clermont-Ferrand
(together with HealthGrid association)
July 18th 2008 – V. Breton