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 multiobjective model for the
problem. In our knowledge, this is a first explored
multiobjective model for the problem. The PARADISEO software
already integrates algorithms to solve multiobjective 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 multiobjective 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 realdata,
especially for anticancer targets such as tubulin.

Comparison with real invitro 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 :
Multiobjective 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 EG. Talbi (LIFL). He is
responsible for overseeing and controlling the management of the
project. He will have overall responsibility the daytoday
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).
