Symbiose seminars

  • TBA

    Hédi Soula (UPMC)
    Thursday, September 20, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    TBA

  • TBA

    Marie Lefebvre (LN2S (Nantes))
    Thursday, May 24, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    TBA

  • Semantic Web of Linked Data

    Olivier Corby (Inria sophia/nice)
    Thursday, April 5, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    En introduction nous rappelons très brièvement les principes du Web sémantique et du Web de données.
    Puis nous présentons deux langages complémentaires issus de nos recherches sur le Web sémantique.
    Le premier langage est STTL, SPARQL Template Transformation Language. Il permet d'écrire des transformations de graphes RDF vers des formats texte tels que Turtle, RDF/XML,  OWL functional syntax,  HTML, etc. 
    Le second est LDScript, Linked Data Script Language, un DSL dédié à la définition de fonctions d'extension pour SPARQL qui ne nécessite pas de compilation. Il permet  d'exécuter des requêtes SPARQL select et construct et de manipuler les résultats. Les objets du langages sont les  graphes, les triplets et les termes RDF,  les solutions de requêtes SPARQL et des listes de tels objets. Il offre des fonctions du second ordre: funcall, apply, map, reduce.

  • Decentralized Data Management for the Semantic Web

    Hala Skaf-Molli et Pascal Molli
    Thursday, March 29, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    The semantic web is an extension of the web where information has a precise meaning. Thousands of linked datasets are available on the web. Important problems concerning quality, deep web access and availability still unsolved. For data quality, we propose to transform the web of data into a read/write web of data. A data consumer will able to correct an error. Allowing consumers to write the semantic web poses the problem of data consistency. We define synchronization algorithms for RDF data model. To access to the deep web, we propose a mediator approach allowing to combine semantic data and deep web data. The problem is to improve the performance of queries in the presence of a large number of data sources. Finally, to ensure the availability, we propose a replication model for the web of data. The problem is to optimize federated SPARQL queries in the presence of replicas selected at queries execution time.

     
     In this talk, we will present our contribution concerning  the deep web access and data availability in the semantic web.
  • A metagenomics (and few other things) perspective on the "star" diatom Asterionella formosa

    Adrien Villain (IGS CNRS)
    Tuesday, March 27, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    Diatoms are unicellular microalgae often found in association with numerous bacterial partners. These interactions may be beneficial, neutral or detrimental, and may evolve over time depending on environmental conditions. Here I will describe how we used laboratory techniques, metagenomics and 16S barcoding to characterize the bacterial community of a non-model freshwater species, Asterionella formosa. Emphasis will be put on the technical challenges of metagenomics assembly, an assessment of the pros and cons of the methods we used, and our recent collaborative work on the prediction of metabolic complementarities within the community.

  • TBA

    Sèverine Bérard (université Montpellier)
    Thursday, March 15, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    TBA

  • A metagenomics (and few other things) perspective on the "star" diatom Asterionella formosa

    Adrien Villain (Information génomique et structurale, CNRS Marseille)
    Thursday, February 22, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    Diatoms are unicellular microalgae often found in association with numerous bacterial partners. These interactions may be beneficial, neutral or detrimental, and may evolve over time depending on environmental conditions. Here I will describe how we used laboratory techniques, metagenomics and 16S barcoding to characterize the bacterial community of a non-model freshwater species, Asterionella formosa. Emphasis will be put on the technical challenges of metagenomics assembly, an assessment of the pros and cons of the methods we used, and our recent collaborative work on the prediction of metabolic complementarities within the community.

  • Genome assembly and bioinformatics with haplotypes

    Bernardo Clavijo (Earlham Institute)
    Thursday, February 15, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    Producing and analysing de novo assemblies of complex organisms is now common across all life sciences. Still, these assemblies are mostly collapsed mosaics representing all haplotypes in single assembled regions. An excessive focus on contiguity has left precision and haplotype phasing as secondary concerns, despite advances in sequencing technologies that generate unprecedented amounts of information about haplotype composition.Here we will explore the possibilities and limitations of haplotype reconstruction on genome assembly, and the current trade-offs on assembly methods in different scenarios such as heterozygous and polyploid samples with short, long and linked reads. We will describe problems and solutions for the reconstruction and analysis of haplotypes in genome graphs. Finally, we will highlight the convergence of genetic and genomic evidence for haplotype studies and conclude with our vision of how the field could evolve in the near future. 

  • Séminaire des CDD Symbiose 2018

    seminaireCDD
    Thursday, February 8, 2018 - 14:15 to 18:00
    Room Markov
    Talk abstract: 

    14h - 14h20 Présentation des équipes 

     

    14h 20 - 16h Présentations de quelques travaux dans Symbiose

     
    • Wesley Delage, "Le Benchmarking, de la bonne initiative aux dérives"
    • Lucas Bourneuf, "Comment j'ai mangé mes données"
    • Camille Marchet, "Retours sur une thèse chez GenScale"
    • Jérémy Gauthier,  "Et si on continuait à faire de la recherche ?"
    • Joseph Kervellec et Chloé Riou, présentation des services développés par Genouest
    16 h break sucré
     
    16h30 - 17 h Présentation association & projet (Nicomaque,SEC, journal club...)
     
    17h - 18h Table ronde
    • Partage d'expérience, questions relatives au monde de la recherche, vie dans Symbiose

     

  • Exploring metabolic modulations using genome-scale network modelling and omics data in the context of toxicological studies: application for deciphering metabolic shifts occurring during the differentiation of the human hepatic cell line HepaRG

    Nathalie Poupin (INRA)
    Thursday, February 8, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    Many man-made chemicals present as contaminants in food and/or water are strongly suspected to induce adverse metabolic effects in Human. Liver is the key organ for xenobiotics biotransformation, and the use of metabolically competent cell lines is essential to explore the mechanisms underlying the metabolic effects of these substances. The hepatic cell line HepaRG, which is increasingly used in toxicity studies, has the particularity to differentiate from progenitor to mature hepatocyte-like cells. We combined multi-omics data and in silico methods in order to better characterize the metabolic capacities of this cell line and to explore the metabolic shifts occurring during this differentiation process. We integrated transcriptomic and metabolomic data in the context of the global human genome-scale metabolic network Recon2, which gathers the metabolic reactions the organism can perform and their associated genes, to compute a relevant sub-network, more specifically representing the functional hepatic metabolic network of HepaRG cells at each developmental stages: day 3 (progenitors) and day 30 (differentiated cells). We used a modified version of the iMAT algorithm developed by Shlomi et al. to identify, based on these data, the sub-networks of reactions specifically active in HepaRG cells at each developmental stage. For each stage, we identified several sub-networks of active reactions, having an equivalent adequacy to experimental data. We applied classification analysis methods to explore intra- and inter-stages variability among these sub-networks. We showed that, for each stage, the heterogeneity between sub-networks was mainly caused by the occurrence of several alternative reactions or the relative low contribution of transcriptomic data in some pathways. To better characterize the systemic metabolic capacities of the cells, we chose, contrary to most approaches, to consider the whole set of similarly adequate sub-networks, since it allows taking into account various metabolic alternatives. Through simulations and pathway enrichment analyses, we predicted that differentiated cells would globally be able to perform a larger number of liver-specific functions (e.g., urea production) and we identified several sets of reactions that were differently active between the two stages. These reactions mostly belong to pathways specific to hepatic activity (e.g., bile acid synthesis) but also to fatty acid synthesis and oxidation pathways. About 50% of the predicted modulated reactions were not evidenced from transcriptomic data and were « newly » inferred by the computational models. Globally, we showed that combining in silico methods with omics data enables to characterize global shifts in the developing hepatic metabolic network.

     

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