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 1 to 30 publications on 153 in total

Haemolysis overestimates plasma oxidative stress biomarkers in free-ranging roe deer

Amandine Herrada, Pauline Vuarin, François Débias, Alexia Gache, Philippe Veber, Maryline Pellerin...

Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology . 298 : 111750

DOI: 10.1016/j.cbpa.2024.111750

Journal article

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ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Stéphane Dray, Anne-Béatrice Dufour, Jean Thioulouse, Aurélie Siberchicot, Thibaut Jombart, Sandrine Pavoine...

Software

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Extraire automatiquement des informations de décisions des juges aux affaires familiales ?

Julien Barnier

Justice et numérique. Quels (r)apports ? . 1

Book chapter

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Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum

Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël...

Peer Community Journal . 3 : e41

DOI: 10.24072/pci.microbiol.100003

Journal article

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The for gene as one of the drivers of foraging variations in a parasitic wasp

Aurore Gallot, Emmanuel Desouhant, Vincent Lhuillier, David Lepetit, Adil El Filali, Laurence Mouton...

Molecular Ecology . 32 ( 7 ) : 1760-1776

DOI: 10.1111/mec.16834

Journal article

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Larval density in the invasive Drosophila suzukii : Immediate and delayed effects on life‐history traits

Alicia Reyes‐ramírez, Zaïnab Belgaidi, Patricia Gibert, Thomas Pommier, Aurélie Siberchicot, Laurence Mouton...

Ecology and Evolution . 13 ( 8 ) : e10433

DOI: 10.1002/ece3.10433

Journal article

see the publication

The for gene as one of the drivers of foraging variations in a parasitic wasp

Aurore Gallot, Emmanuel Desouhant, Vincent Lhuillier, David Lepetit, Adil El Filali, Laurence Mouton...

Molecular Ecology . 32 ( 7 ) : 1760-1776

DOI: 10.1111/mec.16834

Journal article

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The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, Aline Muyle...

: 1-23

DOI: 10.1101/2023.09.21.558754

Preprint

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Population genomics of Corsican wildcats: Paving the way toward a new subspecies within the Felis silvestris spp. complex?

Elodie Portanier, Hélène Henri, Pierre Benedetti, Frédéric Sanchis, Corinne Régis, Pascale Chevret...

Molecular Ecology . 32 ( 8 ) : 1908-1924

DOI: 10.1111/mec.16856

Journal article

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Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus

Djivan Prentout, Aline Muyle, Niklaus Zemp, Adil El Filali, Bastien Boussau, Pascal Touzet...

DOI: 10.1101/2023.10.02.560480

Preprint

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Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

Journal article

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The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Noa Rigoudy, Gaspard Dussert, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Jérome Boyer...

European Journal of Wildlife Research . 69 : 24 p.

DOI: 10.1007/s10344-023-01742-7

Journal article

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DRomics, a workflow to exploit dose-response omics data in ecotoxicology

Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir

Peer Community Journal . 3 : e90

DOI: 10.24072/pcjournal.325

Journal article

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Larval density in the invasive Drosophila suzukii : Immediate and delayed effects on life‐history traits

Alicia Reyes‐ramírez, Zaïnab Belgaidi, Patricia Gibert, Thomas Pommier, Aurélie Siberchicot, Laurence Mouton...

Ecology and Evolution . 13 ( 8 ) : e10433

DOI: 10.1002/ece3.10433

Journal article

see the publication

The for gene as one of the drivers of foraging variations in a parasitic wasp

Aurore Gallot, Emmanuel Desouhant, Vincent Lhuillier, David Lepetit, Adil El Filali, Laurence Mouton...

Molecular Ecology . 32 ( 7 ) : 1760-1776

DOI: 10.1111/mec.16834

Journal article

see the publication

Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum

Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël...

Peer Community Journal . 3 : e41

DOI: 10.24072/pcjournal.269

Journal article

see the publication

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

Journal article

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Neural Networks beyond explainability: Selective inference for sequence motifs

Antoine Villié, Philippe Veber, Yohann de Castro, Laurent Jacob

Transactions on Machine Learning Research Journal .

DOI: 10.48550/arXiv.2212.12542

Journal article

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Transcriptome-wide deregulation of gene expression by artificial light at night in tadpoles of common toads

Morgane Touzot, Tristan Lefebure, Thierry Lengagne, Jean Secondi, Adeline Dumet, Lara Konecny-Dupre...

Science of the Total Environment . 818 : 151734

DOI: 10.1016/j.scitotenv.2021.151734

Journal article

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Extraire des informations fiables des décisions de justice dans une perspective prédictive : des obstacles techniques et des obstacles théoriques

Isabelle Sayn, Julien Barnier, Bruno Jeandidier

Jurimétrie - Revue de la mesure des phénomènes juridiques . ( 2 )

Journal article

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rbioacc: An R-package to analyze toxicokinetic data

Aude Ratier, Virgile Baudrot, Miléna Kaag, Aurélie Siberchicot, Christelle Lopes, Sandrine Charles

Ecotoxicology and Environmental Safety . 242 : 113875

DOI: 10.1016/j.ecoenv.2022.113875

Journal article

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Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions

Stéphanie Jacquet, Michelle Culbertson, Chi Zhang, Adil El Filali, Clément de la Myre Mory, Jean-Baptiste Pons...

Science Advances . 8 ( 47 )

DOI: 10.1126/sciadv.add7540

Journal article

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Meta-transcriptomics reveals stress adaptation processes in microbial communities differing in exposure history

Floriane Larras, Elise Billoir, Stefan Lips, Stephan Schreiber, Philippe Veber, Marie Laure Delignette-Muller...

"Ecology and Evolution: New perspectives and societal challenges" SFE2-GfÖ-EEF joint meeting, International conference on ecological sciences .

Conference paper

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The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images

Noa Rigoudy, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Yoann Bollet, Yoann Bunz...

DOI: 10.1101/2022.03.15.484324

Preprint

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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

Journal article

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Taking full advantage of modelling to better assess environmental risk due to xenobiotics

Sandrine Charles, Aude Ratier, Virgile Baudrot, Gauthier Multari, Aurélie Siberchicot, Dan Wu...

Environmental Science and Pollution Research .

DOI: 10.1007/s11356-021-15042-7

Journal article

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