The workpackages of the project are summarized in the tables below :
Workpackage
Number
|
Workpackage
Title
|
Lead
contactor
|
Start
Month
|
End
Month
|
Deliverable
Number
|
WP1
|
Models
|
IBL
|
0
|
21
|
D1
|
WP2
|
Algorithms
|
LIFL
|
6
|
30
|
D2
|
WP3
|
Gridification
|
LIFL
|
0
|
30
|
D3
|
WP4
|
Validation
& application
|
CEA
|
12
|
36
|
D4
|
WP5
|
Dissemination
|
LIFL+IBL+CEA
|
12
|
36
|
D5
|
Workpackage
WP1
|
Mathematical
models for conformational sampling and docking
|
Participants
|
IBL, CEA
|
Objectives
|
|
Description
of the work
|
Specification of the mathematical models for the
problem. An important point is the flexibility of the
PARADISEO software for optimization which allows to solve
different problems.
Extension towards a multi-objective model for the
problem. In our knowledge, this is a first explored
multi-objective model for the problem. The PARADISEO software
already integrates algorithms to solve multi-objective problems.
Comparison and analysis of different models used for the problem.
|
Deliverables
|
D1.1,
D1.2
|
Workpackage
WP2
|
Optimization
algorithms
|
Participants
|
LIFL, IBL
|
Objectives
|
Design of hybrid and
adaptive techniques.
|
Description
of the work
|
Adapt different metaheuristics to solve the problem
(genetic algorithms, local search).
Design of specific coding and operators for the
problem and their evaluation.
Development of efficient hybrid methods to solve
the problem.
Integration of adaptive techniques for automatic
generation of the different parameters of the methods (crossover
and mutation rate, hybridization, …).
Using advanced multi-objective solvers for the
problem.
We note that all the algorithms will be implemented
under the PARADISEO framework which is a generic software for
optimization problems.
|
Deliverables
|
D2.1,
D2.2
|
Workpackage
WP3
|
Gridification
|
Participants
|
LIFL
|
Objectives
|
Evaluation of the
algorithm’s implementation.
|
Description
of the work
|
Design and implementation of the framework
PARADISEO on Grids using for example Globus and Condor
(PARADISEO@GRID). This work is independent from the docking
problem. So, the results here may be used for any optimization
problem and then for different communities.
Evaluating the deployment of PARADISEO@GRID on
different platforms (GRID’5000, Desktop computing) on classical
combinatorial optimization problems.
Deploy
the designed distributed cooperative algorithms for the docking
problem under PARADISEO@GRID (Docking@Grid).
Evaluation
of the framework Docking@Grid
on different Grid platforms (GRID’5000, Desktop computing).
|
Deliverables
|
D3.1,
D3.2
|
Workpackage
WP4:
|
Validation
and Applications
|
Participants
|
IBL, CEA
|
Objectives
|
Comparison with
other projects and software (EGEE FP6 project, CHARMM, Decrypton,
…).
|
Description
of the work
|
Validation of the results on well known academic
benchmarks.
Application of the software on real-data,
especially for anti-cancer targets such as tubulin.
-
Comparison with real in-vitro screening data.
|
Deliverables
|
D4.1
|
Workpackage
WP5
|
Dissemination
|
Participants
|
IBL,
LIFL, CEA
|
Objectives
|
Disseminate information to
all members of the consortium in order to minimize technical
problems.
Form a user group to
bootstrap a support community.
Disseminate results through
a user group to improve the worth of such information.
Disseminate
project achievements to a wider community.
|
Description
of the work
|
IBL
forms a user group for the software Docking@Grid
Project manager establishes
working practise for mailing lists and meetings.
CEA runs 2 day workshop for
consortium.
User group review evaluation
reports (IBL, CEA).
Tutorials at conferences
(IBL, LIFL).
Software
demonstrations at conferences (IBL, LIFL).
|
Deliverables
|
D5.1,
D5.2
|
The following deliverables will be produced :
Deliverable
|
Workpackage
|
Title
|
Due date
|
Contact
|
D1.1
|
WP1
|
Optimization models used for the
problem
|
T+6
|
IBL
|
D1.2
|
WP1
|
Comparison of the different models
for the problem
|
T+30
|
IBL
|
D2.1
|
WP2
|
Optimization algorithms designed
|
T+12
|
LIFL
|
D2.2
|
WP2
|
Hybrid, adaptive and
parallel cooperative algorithms designed
|
T+21
|
LIFL
|
D3.1
|
WP3
|
Open source
distribution of PARADISEO@GRID
|
T+12
|
LIFL
|
D3.2
|
WP3
|
Open
source distribution of Docking@Grid
|
T+30
|
IBL
|
D4.1
|
WP4
|
Validation and
application results
|
T+24
|
CEA
|
D5.1
|
WP5
|
Dissemination plan
|
T+12
|
CEA
|
D5.2
|
WP5
|
Dissemination report
|
T+36
|
LIFL
|
The
tasks and subtasks of the project during the 36 lifetime months are
summarized in the diagram below. For each subtask, we specify its
initial date, final date, and the research team affected to the task.
We use the following abreviation for the tasks : PM (WP1) :
Problem Modeling ; OS (WP2) : Optimization and Simulation ;
GD (WP3) : Grid Deployment ; VA (WP4) : Validation
and Applications.
→
3
|
→
6
|
→
9
|
→
12
|
→
15
|
→
18
|
→
21
|
→
24
|
→
27
|
→
30
|
→
33
|
→
36
|
PM1 :
Combinatorial optimization modeling of the problem (IBL + LIFL)
|
|
|
|
|
PM2 :
Multi-objective optimization modeling of the problem (LIFL+IBL)
|
|
|
|
|
|
|
|
PM3
: Comparison and validation of differents models (CEA + IBL)
|
|
|
OS1 :
Development of the optimization algorithms (IBL + LIFL)
|
|
|
|
|
OS2 : Design
of the distributed algorithm (LIFL)
|
|
|
|
|
|
|
|
OS3
: Improvements of the optimization algorithms (hybrid, adaptive,
…) ((LIFL, IBL, CEA)
|
GD1 :
PARADISEO Deployment on the GRID (LIFL)
|
|
|
|
|
GD
2 : Gridification of the algorithms under PARADISEO (LIFL)
|
|
|
|
|
VA
1: Validation on well known benchmarks (IBL + CEA)
|
|
|
|
|
|
|
|
|
VA2 :
Integration of the different works and application on real data
(LIFL, IBL, CEA)
|
Project Management : The management of the
project will be the responsibility of E-G. Talbi (LIFL). He is
responsible for overseeing and controlling the management of the
project. He will have overall responsibility the day-to-day
management as defined in the different workpackages of the project.
The project will be organized around a project management committee
(PMC) representing one member from each partner. It will approve all
deliverables and management reports. It will meet at least twice a
year. A web site will host all the information of the project
(deliverable, reports, papers, benchmarks, programs, etc).
|