Computing services

Members

 

info@listes-lbbe.univ-lyon1.fr

 

 

The "Pôle informatique" (hereafter called "PI") is constituted of 8 engineers (1T, 4IE, 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 1 to 30 publications on 161 in total

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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Beyond accuracy : score calibration in deep learning models for camera trap image sequences

Gaspard Dussert, Simon Chamaillé-Jammes, Stéphane Dray, Vincent Miele

DOI: 10.1101/2023.11.10.566512

Preprint

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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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Nine tips for ecologists using machine learning

Marine Desprez, Vincent Miele, Olivier Gimenez

Preprint

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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 .

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 .

Journal article

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Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Marc Ohlmann, Catherine Matias, Giovanni Poggiato, Stéphane Dray, Wilfried Thuiller, Vincent Miele

Ecological Modelling . 483 : 110424

DOI: 10.1016/j.ecolmodel.2023.110424

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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Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks

Julie J. Aubert, Pierre M Barbillon, Sophie Donnet, Vincent Miele

Statistical Approaches for Hidden Variables in Ecology. . : 117-134

DOI: 10.1002/9781119902799.ch6

Book chapter

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An appraisal of graph embeddings for comparing trophic network architectures

Christophe Botella, Stéphane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller

Methods in Ecology and Evolution . 13 ( 1 ) : 203-216

DOI: 10.1111/2041-210X.13738

Journal article

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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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Core-periphery structure in mutualistic networks: an epitaph for nestedness?

Ana Martín González, Diego Vázquez, Rodrigo Ramos-Jiliberto, Sang Hoon Lee, Vincent Miele

DOI: 10.1101/2020.04.02.021691

Preprint

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DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13323

Journal article

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Lifespan decreases with proportion of sons in males but not females of zoo‐housed tigers and lemurs

Morgane Tidière, Guillaume Douay, Peter Müller, Aurélie Siberchicot, Alexander Sliwa, Mylisa Whipple...

Journal of Evolutionary Biology .

DOI: 10.1111/jeb.13793

Journal article

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Sex‐specific actuarial and reproductive senescence in zoo‐housed tiger ( Panthera tigris ): The importance of sub‐species for conservation

Morgane Tidière, Peter Müller, Alexander Sliwa, Aurélie Siberchicot, Guillaume Douay

Zoo Biology .

DOI: 10.1002/zoo.21610

Journal article

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Revisiting animal photo-identification using deep metric learning and network analysis

Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé, Christophe Bonenfant

Methods in Ecology and Evolution . 12 ( 5 ) : 863-873

DOI: 10.1111/2041-210X.13577

Journal article

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Anticoagulation prior to hospitalization is a potential protective factor for COVID-19: insight from a French multicenter cohort study

Richard Chocron, Vincent Galand, Joffrey Cellier, Nicolas Gendron, Thibaut Pommier, Olivier Bory...

Journal of the American Heart Association . 10 ( 8 ) : e018288

DOI: 10.1161/JAHA.120.018624

Journal article

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Images, écologie et deep learning

Vincent Miele, Stéphane Dray, Olivier O. Gimenez

Regards sur la biodiversité .

Journal article

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Revisiting giraffe photo-identification using deep learning and network analysis

Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé, Christophe Bonenfant

DOI: 10.1101/2020.03.25.007377

Preprint

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Journal article

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Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates

Rylan Shearn, Alison E Wright, Sylvain Mousset, Corinne Régis, Simon Penel, Jean-François Lemaître Lemaître...

eLife . 9

DOI: 10.7554/eLife.63650

Journal article

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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel...

Genome Biology and Evolution . ( evaa258 )

DOI: 10.1093/gbe/evaa258

Journal article

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The diversity of interaction types drives the functioning of ecological communities

Vincent Miele, Christian Guill, Rodrigo Ramos-Jiliberto, Sonia Kéfi

DOI: 10.1101/411249

Preprint

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Core–periphery dynamics in a plant–pollinator network

Vincent Miele, Rodrigo Ramos‐jiliberto, Diego Vázquez

Journal of Animal Ecology . 89 ( 7 ) : 1670-1677

DOI: 10.1111/1365-2656.13217

Journal article

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