Organization
 

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

  • Modeling the problem as a combinatorial optimization problem.

  • Analysis of different models such as multi-objective one.

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 optimization algorithms (metaheuristics) to solve the problem.

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

  • Design of distributed and cooperative optimization methods.

  • Deploy the algorithms on Grids.

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

  • Biological validation of the results.

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).