Computing services
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CNRS
Tel: 04 72 44 81 42

Ingénieur d'études
CNRS
Tel: 33 04 72 43 11 68

Ingénieur d'études
CNRS
Tel: 04 72 43 35 82

Technicien
UCBL
Tel: 33 04 72 43 29 04

Ingénieur de recherche
CNRS
Tel: 33 04 72 44 85 44

Ingénieur d'études
CNRS
Tel: 33 04 72 43 29 04

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CNRS
Tel: 33 04 72 43 29 07

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CNRS
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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.

- 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
Molecular Biology and Evolution . 40 ( 2 )
Journal article
see the publicationBeyond accuracy : score calibration in deep learning models for camera trap image sequences
Preprint
see the publicationThe DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images
European Journal of Wildlife Research . 69 : 24 p.
Journal article
see the publicationDRomics, a workflow to exploit dose-response omics data in ecotoxicology
Peer Community Journal . 3 : e90
Journal article
see the publicationPhylteR: efficient identification of outlier sequences in phylogenomic datasets
Molecular Biology and Evolution .
Journal article
see the publicationNeural Networks beyond explainability: Selective inference for sequence motifs
Transactions on Machine Learning Research Journal .
Journal article
see the publicationQuantifying the overall effect of biotic interactions on species distributions along environmental gradients
Ecological Modelling . 483 : 110424
Journal article
see the publicationMeta-transcriptomics reveals stress adaptation processes in microbial communities differing in exposure history
"Ecology and Evolution: New perspectives and societal challenges" SFE2-GfÖ-EEF joint meeting, International conference on ecological sciences .
Conference paper
see the publicationtidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
Journal article
see the publicationThe DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images
Preprint
see the publicationChapter 6: Using Latent Block Models to Detect Structure in Ecological Networks
Statistical Approaches for Hidden Variables in Ecology. . : 117-134
Book chapter
see the publicationBayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
Journal article
see the publicationAn appraisal of graph embeddings for comparing trophic network architectures
Methods in Ecology and Evolution . 13 ( 1 ) : 203-216
Journal article
see the publicationThirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Bioinformatics . 38 ( 8 ) : 2350–2352
Journal article
see the publicationTaking full advantage of modelling to better assess environmental risk due to xenobiotics
Environmental Science and Pollution Research .
Journal article
see the publicationCore-periphery structure in mutualistic networks: an epitaph for nestedness?
Preprint
see the publicationDILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Journal article
see the publicationLifespan decreases with proportion of sons in males but not females of zoo‐housed tigers and lemurs
Journal of Evolutionary Biology .
DOI: 10.1111/jeb.13793
Journal article
see the publicationSex‐specific actuarial and reproductive senescence in zoo‐housed tiger ( Panthera tigris ): The importance of sub‐species for conservation
Zoo Biology .
DOI: 10.1002/zoo.21610
Journal article
see the publicationRevisiting animal photo-identification using deep metric learning and network analysis
Methods in Ecology and Evolution . 12 ( 5 ) : 863-873
Journal article
see the publicationAnticoagulation prior to hospitalization is a potential protective factor for COVID-19: insight from a French multicenter cohort study
Journal of the American Heart Association . 10 ( 8 ) : e018288
Journal article
see the publicationRevisiting giraffe photo-identification using deep learning and network analysis
Preprint
see the publicationDeep learning for species identification of modern and fossil rodent molars
Preprint
see the publicationTreerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Journal article
see the publicationEvolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates
eLife . 9
DOI: 10.7554/eLife.63650
Journal article
see the publicationEvolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species
Genome Biology and Evolution . ( evaa258 )
DOI: 10.1093/gbe/evaa258
Journal article
see the publicationThe diversity of interaction types drives the functioning of ecological communities
DOI: 10.1101/411249
Preprint
see the publicationCore–periphery dynamics in a plant–pollinator network
Journal of Animal Ecology . 89 ( 7 ) : 1670-1677
Journal article
see the publication