Symbiose seminars

  • Genome scale metabolic modeling and study of secondary metabolism of 24 Penicillium species

    Sylvain Prigent
    Thursday, May 31, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    During this presentation I will talk about my 3 years of Postdoc in Jens Nielsen lab in Sweden. Where I studied metabolism of Penicillium species. Modelling of metabolism at the genome scale have proved to be an efficient for explaining observed phenotypic traits in living organisms. Further, it can be used as a means of predicting the effect of genetic modifications e.g. for generation of microbial cell factories. With the increasing amount of genome sequencing data available, a need exists to accurately and efficiently generate such genome scale metabolic models (GEMs) of non-model organisms, for which there are few data. In this talk, I will present a semi-automatic reconstruction approach applied to 24 Penicillium species, which have potential for production of pharmaceuticals secondary metabolites or used in foods such as cheeses. The models were based on the MetaCyc database and a previously published Penicillium GEM, and gave rise to comprehensive genome scale descriptions of their metabolism. The models proved that while central carbon metabolism is highly conserved, secondary metabolic pathways represent the main diversity among the species. I will also present some work we did on prediction of production of secondary metabolites based on genomic sequence and some RNA-seq analysis on those 24 species.

    At the end of my presentation I will also talk a little about my current and future work on fruit biology at INRA Bordeaux.

     

  • BRAvo : A tool for regulatory network assembly through Linked Open Data

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

    A few years ago, SyMeTRIC health actors have proposed personalized medicine approaches in the context of several pathologies or therapeutical approaches such as cancer, transplantation, cardiovascular, respiratory or metabolic diseases. In spite of pathological diversities, these actors share methodological and technological commonalities. In particular they strongly rely on the exploration and combination of several heterogeneous and massive biological and clinical datasets to discover multi-parameter pathological signatures and new biomarkers.

    In order to assemble data arising from different scales, technologies or localities, huge efforts address the organization of biological knowledge through linked open databases. These databases are supposed to be automatically queryable in order to reconstruct regulatory and signaling networks. Nevertheless, assembling networks usually implies manual operations due to source-specific identification of biological entities and relationships, multiple life-science databases with redundant information and difficulty to recover the logical flow of a biological pathway.

    In this talk, I will provide a framework based on Semantic Web technologies for automating the assembly of regulatory and signaling networks. To this purpose,  I developed BRAvo, an interactive web tool, allowing users to interact with the reconstruction process, and a command-line tool allowing to address larger scale models in a batch mode.

    Our results show that BRAvo is able to retrieve networks of 5000 nodes from 200 input genes by querying the full PathwayCommons database in less than one hour. BRAvo can also provide interesting filters of data sources, depth reconstruction and biological entities type. Thanks to BRAvo, we are now able to address issues of heterogeneous data integration for biological network reconstruction intended for computational and predictive models.

  • De la reconstruction de génomes ancestraux vers l'aide à l'assemblage

    Sèverine Bérard (Institut des Sciences de l'Evolution - Montpellier)
    Thursday, May 17, 2018 - 10:30
    Room Minquiers
    Talk abstract: 

    Nous présenterons une méthode permettant de reconstruire des génomes ancestraux dans un contexte phylogénétique. Cette approche retrace l'histoire évolutive des adjacences de gènes en prenant en entrée les ordres de gènes dans les espèces actuelles et les arbres phylogénétiques des gènes et des espèces, et en optimisant un critère de parcimonie. L'algorithme sous-jacent est basé sur le principe de programmation dynamique, ce qui permet de traiter de gros jeux de données en temps raisonnable. Plusieurs modifications de ce premier algorithme ont permis, entre autre, de reconstruire à la fois les ordres de gènes ancestraux et actuels, permettant ainsi d'améliorer le scaffolding des génomes actuels. La méthode est également capable d'inférer des scores de confiance aux adjacences prédites et de prendre en entrée des données de séquençage appariées. Nous montrerons l'application de notre méthode sur un jeu de données de 18 moustiques Anopheles où nous avons pu réduire le nombre de scaffolds de plus de 60 %. Cette méthode est implémentée dans le logiciel DeCoSTAR (http://pbil.univ-lyon1.fr/software/DeCoSTAR/get.html

  • 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

     

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