Computing services

Members

 

info@listes-lbbe.univ-lyon1.fr

 

 

The "Pôle informatique" (hereafter called "PI") is constituted of 9 engineers (1T, 5IE, 3IR). Our activities are distributed among three main directions: computing and storage infrastructure management (shared resources, and invidual equipment), software and service development and data analysis in molecular biology and ecology.

Infrastructures managment

  • Microcomputing: the PI is in charge of managing the laboratory's microcomputer equipment, from choosing the most appropriate solution in consultation with the future user to managing maintenance, including installation and configuration of the equipment.
  • Laboratory Information System: the PI provides laboratory and community members with a number of services, including several web servers (apache), numerous database servers (relational or indexed) and several collaborative tools (Git, Redmine, Seafile...). These services are hosted on largely virtualized machines.
Cluster de calcul UMR5558/PRABI
  • Compute and storage: since 2009, the PI manages a computing cluster with almost 1200 avalaible computing cores. The cluster is linked to a 600 TB high performing distributed storage system under BeeGFS and an object mode storage based on iRods (~400 useful TB).
  • Cloud and containerization: cloud-girofle (224 vcpu and 120 To), the local cloud operated by the PI since 2017, is part of the Biosphere cloud federation from the French Institute of Bioinformatics (IFB). We are starting to converge our virtualization infrastructure towards containerization technologies (docker, singularity).  
  • User support: the PI provides user support for all the resources and tools available to the laboratory's members. It trains and supports users in their use of shared resources through trainingsessions, information and monitoring meetings and mailing lists.

Software and methodological development

Members of the PI are involved in numerous software development projects in collaboration with the lab researchers, covering a large range of programming languages (R, Python, C++, OCaml, Javascript, SQL, shell). It goes from optimized parallel numerical codes to web services and dedicated databases (SQL or no-SQL). A peculiar effort is also performed to share the best practices of modern software development and make these software codes reproducible and available following the standards and requirements of the community.

Data analysis

Members of the PI are in the front line facing the data avalanche (and the data diversity) of this decade.
A large part of our activity is related to the quantity of data coming from sequencing technologies. The PI develops and proposes pipelines for genomic data assembly and annotation, RNA-seq and RAD-seq data analysis. More recently, computer image processing has become an important issue for future ecological studies performed in the lab in the Evolutionary Ecology.

Animation, training and scientific expertise

Our group has set up a series of dedicated workshops  to improve internal skills in software engineering, distributed computing, programming and data analysis, which complements more formal teaching sessions. Members of the group are also involved in training activities in universities (UCBL1) and CNRS (Formation permanente).
In their respective fields, members of the PI actively monitor technological developments and participate in major events such as JOBIM (bioinfo), the JRES (system administration), the JDEV (development), the Aramis days (system and network administration and software development) and the 'Rencontres R' (programmation). The PI is also involved in dedicated networks and/or projects of national scope such as the LyonCalcul group, the RLyon group and the IFB-NNCR and IFB-Core projects.

We works in close cooperation with the bioinformatics platform PRABI (Pôle Rhône-Alpes de BioInformatique), notably for the management of the computing and storage infrastructure, the diffusion of our lab's software production, the organization of teaching sessions and for sharing expertise in genomic/transcriptomic data analysis.

Poster

Publications

Display of 61 to 90 publications on 153 in total

Response to Comment on "Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Veber

Environmental Science and Technology . 51 : 8202-8203

DOI: 10.1021/acs.est.7b02548

Journal article

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Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Ruiz, P. Veber

Environmental Science and Technology . 51 : 4038-4045

DOI: 10.1021/acs.est.6b05326

Journal article

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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost...

Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431

DOI: 10.1093/gbe/evx255

Journal article

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MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve, Akbar A Rafiey, Adrian A Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau...

DOI: 10.1101/127548

Other publication

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Les Ateliers Pratiques Numériques en SHS des laboratoires lyonnais

Julien Barnier, Séverine Gedzelman, Nicolas Genis, Emmanuelle Morlock, Hervé Parmentier, Samantha Saïdi

Forum Humanités Numériques et données ouvertes .

Poster

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Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies

Samuel Venner, A. Siberchicot, P.F. Pélisson, E. Schermer, Marie-Claude Bel-Venner, M. Nicolas...

The American Naturalist . 188 ( 1 ) : 66-75

DOI: 10.1086/686684

Journal article

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Quantitative Molecular Detection of 19 Major Pathogens in the Interdental Biofilm of Periodontally Healthy Young Adults

Florence Carrouel, Stéphane Viennot, Julie Santamaria, Philippe Veber, Denis Bourgeois

Frontiers in Microbiology . 7 : 840 - 840

DOI: 10.3389/fmicb.2016.00840

Journal article

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

Journal article

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No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Clémentine François, L. Duret, Laurent Simon, Florian Mermillod-Blondin, Florian Malard, Lara Konecny-Dupré...

Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620

DOI: 10.1093/molbev/msw131

Journal article

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L'enseignement et la formation au logiciel R : un retour d'expérience

Julien Barnier

Séminaire "R à l'usage des sciences sociales" (RUSS) .

Conference paper

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RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements

Amandine Chatagnon, Philippe Veber, Valérie Morin, Justin Bedő,, Gérard Triqueneaux, Marie Sémon...

Nucleic Acids Research . 43 ( 10 ) : 4833--4854

DOI: 10.1093/nar/gkv370

Journal article

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Unknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions.

Eléonore Hellard, Dominique Pontier, Aurélie Siberchicot, Frank Sauvage, David Fouchet

Epidemics . 11 : 48-55

DOI: 10.1016/j.epidem.2015.02.004

Journal article

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Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri, Marie Cariou, Gabriel Terraz, Sonia Martinez, Adil El Filali, Marine Veyssière...

Genetica . 143 ( 2 ) : 139-143

DOI: 10.1007/s10709-015-9828-3

Journal article

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Générer des documents avec RMarkdown

Julien Barnier

Rencontre du groupe des utilisateurs de R sur Lyon .

Conference paper

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From bicycle sharing system movements to users: a typology of Vélo’v cyclists in Lyon based on large-scale behavioural dataset

Marie Vogel, Ronan Hamon, Guillaume Lozenguez, Luc Merchez, Patrice Abry, Julien Barnier...

Journal of Transport Geography . 41 : 280-291

DOI: 10.1016/j.jtrangeo.2014.07.005

Journal article

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Determining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method

A. Merville, A. Vallier, Samuel Venner, A. Siberchicot, D. Fouchet, A. Heddi...

European Journal of Entomology . 111 ( 4 ) : 567-573

DOI: 10.14411/eje.2014.056

Journal article

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Host plant specialization matters in the epidemiology of Wolbachia across phytophagous wasps (Hymenoptera: Torymidae)

Thomas Boivin, Hélène Henri, Fabrice Vavre, Cindy Gidoin, Philippe Veber, Jean-Noël Candau...

8. International Wolbachia Conference . : np

Poster

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Statistical handling of reproduction data for exposure-response modeling

Marie Laure Delignette-Muller, Christelle Lopes, Philippe Veber, Sandrine Charles

Environmental Science and Technology . 48 : 7544-51

DOI: 10.1021/es502009r

Journal article

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Epidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters.

Thomas Boivin, Hélène Henri, Fabrice Vavre, Cindy Gidoin, Philippe Veber, Jean-Noël Candau...

Molecular Ecology Notes . 23 ( 9 ) : 2362-2375

DOI: 10.1111/mec.12737

Journal article

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Indexation et recodages avec R et questionr

Julien Barnier

Séminaire "R à l'usage des sciences sociales" (RUS) .

Conference paper

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Applications Web avec Shiny

Julien Barnier

Première rencontre du groupe des utilisateurs de R sur Lyon .

Conference paper

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L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

Journal article

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The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle.

Seydina Diene, Vicky Merhej, Mireille Henry, Adil El Filali, Véronique Roux, Catherine Robert...

Molecular Biology and Evolution . 30 ( 2 ) : 369-83

DOI: 10.1093/molbev/mss236

Journal article

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Conference Report: Deuxièmes Rencontres R

Aurélie Siberchicot, S. Dray

The R Journal . 5/2 : 164--165

Journal article

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Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate

Laetitia Rouli, Jean-Marc Rolain, Adil El Filali, Catherine Robert, Didier Raoult

Journal of Bacteriology . 194 ( 24 ) : 6939-6939

DOI: 10.1128/JB.01856-12

Journal article

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BioNLP Shared Task - The Bacteria Track

Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte...

BMC Bioinformatics . 13 : np

DOI: 10.1186/1471-2105-13-S11-S3

Journal article

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Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

Brigitte Mangin, Aurélie Siberchicot, S. Nicolas, Agnes Doligez, Patrice This, Christine Cierco-Ayrolles

Heredity . 108 ( 3 ) : 285-291

DOI: 10.1038/hdy.2011.73

Journal article

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An evaluation of the effects of Lactobacillus ingluviei on body weight, the intestinal microbiome and metabolism in mice

Emmanouil Angelakis, Delphine Bastelica, Amira Ben Amara, Adil El Filali, Anne Dutour, Jean-Louis Mege...

Microbial Pathogenesis . 52 ( 1 ) : 61-68

DOI: 10.1016/j.micpath.2011.10.004

Journal article

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