Docking@GRID

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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).