Projects
Translational informatics
Development of a computational infrastructure dedicated to the integrated analysis of data from "-omics" sciences (cf. www.omics-ethics.org/ fr/definition-science-omics) related to human genetic diseases and health. This infrastructure includes algorithms and original methods, such as:
- Algorithms and workflows for structural bioinformatics, in the context of a project financed by the French Bioinformatics Institute (IFB), coordinated by P. Tufféry (RPBS, Paris) and D. Ritchie (Loria, Nancy).
- Algorithms for integrative structural biology, in the context of ongoing funded projects, including the European INSTRUCT research infrastructure for 'Integrative Structural Biology' and the French ANR Investments for the Future project: FRISBI, coordinated by Bruno Klaholtz, IGBMC, Strasbourg.
- Multi-scale methods for a better understanding of protein properties (structure, interactions, dynamics...) and better integration of the heterogenous data associated with a protein or a family of proteins. Ongoing project, BIPBIP, funded by French ANR in collaboration with Annick Dejaegere, IGBMC, Strasbourg.
- Evolutionary analyses of protein sequences from NGS data, applied to health, in collaboration with the Data_Mining data mining and SONIC teams.
- GREMSAP (GRid Evolutionary Multiple Sequence Alignment Platform), in collaboration with the SONIC team, l’Institut des Systèmes Complexes Paris Île de France, l’Institut de Neurobiologie Albert Fressard.
- Social Network Clinical Database for Intellectual Disabilities: Development of a social network for patients, related to genetic diseases causing developmental disabilities, in collaboration with the SONIC team, the Translational medicine & neurogenetics team, IGBMC, led by Jean-Louis Mandel, and the [http:/www.ucad.sn Cheikh Anta Diop University, Senegal].
- Infrastructure for 'big data' management for the translational analysis of mutations involved in human genetic disease. BIRD/SM2PH-central is aimed at the integration of heterogeneous data (genomic, phenotypic, evolution, cellular networks,...), with data mining methods (association rules, inductive logic programming,...), and includes the design of a semantic query language (BIRD-QL) and the development of original graphical interfaces. These developments are done in collaboration with Hoan Ngyugen, IGBMC, Strasbourg.
Systems bioinformatics
Development of research in the field of biological systems analysis, to understand genotype-phenotype relationships, notable concerning genetic diseases, and the study of complex biological systems, for example in various cancers or rare diseases (ciliopathies, myopathies,...) in close collaboration with the Human Genetics Laboratory, led by Hélène Dollfus (www.unistra.fr/index.php?id=19264&L=3). The originality of our approach lies in the extraction and exploitation of evolutionary information (sequence analysis, comparative genomics, etc.) in order to improve the analysis of the different levels of complexity in biological systems. Some examples of systems-level projects:
- Analysis of macromolecular complexes (TFIID...) in collaboration with the Department of Integrative structural biology, IGBMC.
- Analysis of organelles (exosome, endosome...) in collaboration with the membrane traffic and lipid signaling team, GMGM: synthetic yeast evolution, the characterization of the shared / specific features at different levels (nucleotide, gene, pathway), the identification of correlations between the evolutionary scenarios and the modifications identified in the molecular processes.
- Genomic analysis of 1000 myopathy patients (Myocapture project and ongoing FRM-funded project, in collaboration with le team of Jocelyn Laporte, IGBMC) with the goal of identifying and characterizing new genes in these diseases.
- Analysis of genomic data from ciliopathy patients (Bardet-Biedl Syndrome and Alström Syndrome) to identify the genes responsible for the diseases, and to understand the links between genotypes/phenotypes, in collaboration with Human Genetics Laboratory, led by Hélène Dollfus.
- Integration of "omics" data to develop a new generation of the Vaccinia virus (VACV). Ongoing funded project (OncoVaccine: ANR Recherches Partenariales et Innovation Biomédicale) in collaboration with TRANSGENE, the HTCS platform led by Laurent Brino, IGBMC and the team of Etienne Weiss, IREBS, Strasbourg.
- ImAnno is a collaborative project between the LBGI and teams at the IGBMC, Strasbourg (P. Dollé) and the Institute of Vision, Paris (J. Sahel, T. Leveillard) aimed at developing an ergonomic and integrative annotation tool for biological images (ISH, fundus...). Once annotated, the images allow to access all the knowledge extraction tools implemented or developed by the LBGI, including protein-protein interaction networks, tools for automatic analysis of the evolution, transcriptomic data, etc.
- Multi-scale tempo-spatial modeling of the primary cilia as a means of communication (intracellular transport, physical cell-cell interactions, environmental sensory system) and its role in the cell cycle, development, as well as the evolution of eukaryotic organisms, in collaboration with the Digital Campus for Complex Systems.
Artifical Evolution and Complex Systems
ECOMAPS (Evolutionary Computation on Massively Parallel Systems)
The purpose of the ECOMAPS project is to revisit the different evolutionary paradigms in order to adapt them to massive parallelism, notably on General Purpose Graphic Processing Units (GPGPUs) and to integrate them into the EASEA language(click here for a rapid introduction).
It consists of 3 axes :
Continued development of the language EASEA (EAsy Specification of Evolutionary Algorithms, (Collet et al., 2001) allowing an evolutionary algorithm to be executed on GPGPU cards General Purpose Graphic Processing Unit without the programmer needing to know how to programme the cards. Le développement de la plateforme de calcul évolutionnaire massivement parallèle EASEA est actuellement assuré par :
- Ogier Maitre pour les algorithmes évolutionnaires et la programmation génétique, et
- Frédéric Kruger pour CMA-ES (Covariance Matrix Adapatation Evolutionary Strategy, utilisée pour les problèmes continus), les algorithmes mémétiques(algorithmes hybridés avec une recherche locale pour une évolution Lamarckienne) et la parallélisation en îlots sur clusters de machines hybrides.
La plateforme EASEA intègre les derniers développements algorithmiques de l'équipe. Il est disponible sur Sourceforge.
- - Adaptation de la Programmation Génétique Linéaire à l'exécution sur cartes GPGPU
- La Programmation Génétique Linéaire, développée par Wolfgang Banzhaf (cf. Brameier & Banzhaf, 2007) semble particulièrement bien adaptée à l'architecture des processeurs GPU. Ogier Maitre et Wolfgang Banzhaf travaillent à modifier la Programmation Génétique Linéaire pour profiter des spécificités de ces cartes massivement parallèles. Le résultat sera intégré au langage EASEA (cf. ci-dessous).
- - Implémentation d'un algorithme de chimie virtuelle sur GPGPU
- La chimie virtuelle est un paradigme qui peut servir non seulement à simuler des réactions chimiques, mais qui peut aussi être utilisé pour résoudre des problèmes scientifiques. Le sujet du post-doc de Lidia Yamamoto consiste à porter la chimie virtuelle sur cartes GPU.
ARA (Administrateur Réseaux Artificiel)
- Post-doc de Deepak Sharma financé par OSEO pour la société Kelerio. La société Kelerio administre des réseaux pour des entreprises clientes. Le but du projet ARA est de créer un Administrateur Réseaux artificiel capable de détecter des pannes et d'y remédier avant qu'elles ne surviennent.
Une collaboration a lieu sur ce sujet avec Cécilia Zanni-Merck et Philippe Bouché du LGeCo (INSA de Strasbourg).
RENZEO (Recherche de Nouvelles Zéolites)
Stage de M2 ILC option Recherche faisant suite à un stage de M1 en collaboration avec Laurent Baumes de l'Instituto de Tecnologia Quimica de l'Université Polytechnique de Valencia (Espagne). Les zéolites sont des structures cristallines poreuses d'une grande importance dans l'industrie. Suivant le diamètre des pores de la molécule, une zéolite peut être utilisée comme adsorbant, pour filtrer ou retenir d'autres molécules, permettant ainsi de déshydrater du gaz ou comme catalyseur. Chaque nouvelle découverte de zéolite permet de nouvelles utilisations industrielles, d'où l'importance de la recherche dans ce domaine.
BETON (optimisation de structures béton)
Cédric den Drijver effectue un stage en apprentissage financé par l'INSA de Strasbourg dans le cadre d'une collaboration autour de la thèse de Céline Conrardy financée par Lafarge. Le but de cet apprentissage est d'optimiser des structures béton (poutrelles, par exemple) par Programmation Génétique sur GPGPU en les évaluants par éléments finis.