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.
- 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.
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.
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 )
Beyond accuracy : score calibration in deep learning models for camera trap image sequences
The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images
European Journal of Wildlife Research . 69 : 24 p.
DRomics, a workflow to exploit dose-response omics data in ecotoxicology
Peer Community Journal . 3 : e90
Nine tips for ecologists using machine learning
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Molecular Biology and Evolution .
Neural Networks beyond explainability: Selective inference for sequence motifs
Transactions on Machine Learning Research Journal .
Quantifying the overall effect of biotic interactions on species distributions along environmental gradients
Ecological Modelling . 483 : 110424
Meta-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 .
tidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images
Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks
Statistical Approaches for Hidden Variables in Ecology. . : 117-134
Bayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
An appraisal of graph embeddings for comparing trophic network architectures
Methods in Ecology and Evolution . 13 ( 1 ) : 203-216
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Bioinformatics . 38 ( 8 ) : 2350–2352
Taking full advantage of modelling to better assess environmental risk due to xenobiotics
Environmental Science and Pollution Research .
Core-periphery structure in mutualistic networks: an epitaph for nestedness?
DILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Lifespan decreases with proportion of sons in males but not females of zoo‐housed tigers and lemurs
Journal of Evolutionary Biology .
Sex‐specific actuarial and reproductive senescence in zoo‐housed tiger ( Panthera tigris ): The importance of sub‐species for conservation
Zoo Biology .
Revisiting animal photo-identification using deep metric learning and network analysis
Methods in Ecology and Evolution . 12 ( 5 ) : 863-873
Anticoagulation 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
Images, écologie et deep learning
Regards sur la biodiversité .
Revisiting giraffe photo-identification using deep learning and network analysis
Deep learning for species identification of modern and fossil rodent molars
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates
eLife . 9
Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species
Genome Biology and Evolution . ( evaa258 )
The diversity of interaction types drives the functioning of ecological communities
Core–periphery dynamics in a plant–pollinator network
Journal of Animal Ecology . 89 ( 7 ) : 1670-1677