Computing services

Members

 

info@listes-lbbe.univ-lyon1.fr

 

 

The "Pôle informatique" (hereafter called "PI") is constituted of 8 engineers (1T, 1AI, 3IE, 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 250 TB high performing distributed storage system under BeeGFS and an object mode storage based on iRods (~300 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 156 in total

Calcul parallèle avec R

Vincent Miele, Violaine Louvet

978-2-7598-2060-3

Book

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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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DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity

Monica Naughtin, Zofia Haftek-Terreau, Johan Xavier, Sam Meyer, Maud Silvain, Yan Jaszczyszyn...

PLoS ONE . 10 : e0129427

DOI: 10.1371/journal.pone.0129427

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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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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Spatially constrained clustering of ecological networks

Vincent Miele, Franck Picard, S. Dray

Methods in Ecology and Evolution . 5 ( 8 ) : 771-779

DOI: 10.1111/2041-210X.12208

Journal article

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Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles

Guillem Rigaill, Vincent Miele, Franck Picard

Lecture Notes in Computer Science . 8452 : 248-258

Journal article

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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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Navigating in a Sea of Repeats in RNA-seq without Drowning

Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96

DOI: 10.1007/978-3-662-44753-6_7

Conference paper

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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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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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New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, Marie-France Sagot...

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .

Conference paper

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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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Fast and parallel algorithm for population-based segmentation of copy-number profiles

Guillem Rigaill, Vincent Miele, Franck Picard

10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) . 8452 : 275 p.

DOI: 10.1007/978-3-319-09042-9_18

Conference paper

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Toward community standards in the quest for orthologs

Christophe Dessimoz, Toni Gabaldon, David Roos, Erik L L Sonnhammer, Javier Herrero, Alfonso Valencia...

Bioinformatics . 28 ( 6 ) : 900-904

DOI: 10.1093/bioinformatics/bts050

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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The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis

Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib...

PLoS ONE . 7 ( 2 ) : e31490

DOI: 10.1371/journal.pone.0031490

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

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RENABI GRISBI Infrastructure Distribuée pour la Bioinformatique

Christophe Blanchet, Clément Gauthey, Christophe C. Caron, Olivier Collin, Stephane Delmotte, Tiphaine Martin...

JOBIM 2011 - Journées Ouvertes Biologie Informatique Mathématique .

Conference paper

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PhEVER: a database for the global exploration of virus-host evolutionary relationships.

Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, Christian Gautier

Nucleic Acids Research . 39 ( Database issue ) : D569-75

DOI: 10.1093/nar/gkq1013

Journal article

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Orientia tsutsugamushi Stimulates an Original Gene Expression Program in Monocytes: Relationship with Gene Expression in Patients with Scrub Typhus

Wiwit Tantibhedhyangkul, Thanavadee Prachason, Duangdao Waywa, Adil El Filali, Eric Ghigo, Wanna Thongnoppakhun...

PLoS Neglected Tropical Diseases . 5 ( 5 ) : e1028

DOI: 10.1371/journal.pntd.0001028

Journal article

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Genetic structure and linkage disequilibrium in 4 Vitis species

Patrice This, Stephane Nicolas, Jean-Pierre Peros, Thierry Lacombe, Loic Le Cunff, Jean-Michel Boursiquot...

Plant and Animal Genomes Conference . : np

Conference paper

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BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming

Julien Jourde, Alain-Pierre Manine, Philippe Veber, Karen Fort, Robert Bossy, Erick Alphonse...

Proceedings of the BioNLP Shared Task 2011 ACL Workshop . 13 9781937284091 : 65-73

Conference paper

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