Team Orpailleur

Overall Objectives
Scientific Foundations
Application Domains
New Results
Other Grants and Activities

Section: Other Grants and Activities

International projects and collaborations

The AmSud Project: Semantic-based support for Collaborative Design Activity

Participants : Alexandre Blansché, Amedeo Napoli [ contact person ] , Yannick Toussaint.

The main goal of this cooperation project is to define a methodological and software support for integrating semantic technologies in a collaborative computer-supported design activity. The project intends to demonstrate that semantic web technologies are a suitable and efficient option for improving collaborative computer-assisted design process. Thus, semantic requirements for design situations have to be identified, and, methodological support and software solution for management have to be developed.

There is a need for studying how collaborative design activities can be guided by domain knowledge. Here, domain ontologies have to help designers in assembling design components, in searching adequate components, detecting conflicts, searching related documents, finding people with the adequate skills, etc. The design work can be done by several people distributed over time, space, and organizations. Wikis are very good examples of such distributed activities. Moreover, a special attention is given to semantic wikis: semantic activities for wiki design and wiki management for semantic activities.

This project involves researchers from LORIA (Orpailleur and SCORE teams), LIFIA at Universita de La Plata (Argentina), Laboratório Intermidia at Universidade de Sao Paulo in Sao Carlos (Brazil), and Departamento de Informática de Universidad Técnica Federico Santa María (Santiago do Chile, Valparaiso). Two publications are associated to the project [34] , [61] .

International Collaborations in Biology and Chemistry

Participants : Yasmine Assess, Sid-Ahmed Benabderrahmane, Emmanuel Bresso, Matthieu Chavent, Marie-Dominique Devignes, Léo Gemthio, Anisha Ghoorah, Vincent Leroux, Bernard Maigret, Lazaros Mavridis, Nizar Messai, Dave Ritchie, Vishwesh Venkatraman, Malika Smaïl-Tabbone.

Grand Challenge project - Foundation Bill and Melinda Gates

This collaboration involves the “J. Craig Venter Institute” at Rockville, MD 20850 USA, and the “Centre International de Référence Chantal Biya pour la Recherche sur la Prevention et la Prise en charge du VIH/Sida” (CIRCB), BP 3077, Yaoundé Cameroun. It is entitled “Design and Setting Up of a Bioinformatics Platform Dedicated to HIV Drug Resistance Problems” and ran from September 2008 until September 2009. A joint publication is currently in preparation.

Search for anti-HIV drugs acting as entry-blockers

In collaboration with computational chemistry colleagues at the University of Bari and the Institut Chimique de Sarria (IQS) in Barcelona, Dave Ritchie published a review of the state of in silico protein structure modeling and virtual drug screening techniques regarding the development of CCR5 entry-blockers (major [3] ). As there now exist several hundred CCR5 entry-blockers, there is considerable interest in the chemoinformatics community in how best to use knowledge of known drug molecules to develop new and more potent new drug candidates [90] . In September, Dave Ritchie gave a presentation at the international Modeling-09 conference in Erlangen on recent collaborative work with Violeta Pérez-Nueno of the IQS on clustering and classifying novel CCR5 HIV entry inhibitors using spherical harmonic shape representations [89] . The spherical harmonic clustering approach developed by Dave Ritchie and Violeta Pérez-Nueno was recently used successfully in a virtual screening study at the IQS to discover new high-affinity ligands for CCR4 [31] .

Critical Assessment of Protein-Protein Interactions (CAPRI challenge)

Every two years, the state of the art in protein docking is assessed at the CAPRI (Critical Assessment of PRedicted Interactions ) international conference. For the CAPRI assessments, participants are given the structures or sequences of a pair of proteins that are known to bind but for which the corresponding structure of the complex has not yet been published. Our method combines human expertise, fast rigid-body docking (using Hex program) and molecular dynamics. This strategy produced good results for several targets (Target 34: our predictions were amongst the best for this target according to the ligand RMSD criteria ; Target 40: we identified key residues before they were revealed by the organisers thanks to litterature and analogues interactions). It was presented as a poster at the 4th CAPRI Evaluation Meeting in Barcelona in December 2009.

Other international collaborations

Participants : Mehdi Kaytoue, Amedeo Napoli.

Two close international research collaborations have to be still mentioned: (i) one with Petko Valtchev at Université du Québec à Montréal (UQAM) and Marianne Huchard at LIRMM Montpellier, (ii) the other with Sergei Kusnetsov at Higher School of Economics in Moscow (HSE). The two collaborations are based on visits in the different laboratories and in the writing of common papers. The research topic in (i) holds on the design of algorithms for itemset search and association rule extraction, and the design of large concept lattices and relational concept lattices (major [10] ). The research topic in (ii) holds on extension of FCA algorithms for taking into account complex data (major [6] ).


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