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.
- 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 139 in total
Revisiting animal photo-identification using deep metric learning and network analysis
Methods in Ecology and Evolution . 12 ( 5 ) : 863-873
An appraisal of graph embeddings for comparing trophic network architectures
Methods in Ecology and Evolution .
Quantifying the overall effect of biotic interactions on species communities along environmental gradients
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 .
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 . : e018288
DILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
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
IFB-Biosphère : Services cloud pour l'analyse des données des sciences de la vie
Journées RESeaux - JRES 2019 .
CAARS: comparative assembly and annotation of RNA-Seq data
Bioinformatics . 35 ( 13 ) : 2199-2207
Detecting adaptive convergent amino acid evolution
Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11
Nine Quick Tips for Analyzing Network Data
PLoS Computational Biology . 15 ( 12 ) : e1007434
Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model
PLoS Computational Biology . 15 ( 8 ) : e1007269
Diversity indices for ecological networks: a unifying framework using Hill numbers
Ecology Letters . 22 ( 4 ) : 737-747
Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Pollen limitation as a main driver of fruiting dynamics in oak populations
Ecology Letters . 22 ( 1 ) : 98-107
MOSAIC : une plate-forme web pour l’analyse statistique des données d’écotoxicologie. Fiche Thématique N°13
: 4 p.
Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis
mSystems . 3 ( 5 )
Maternal reproductive senescence shapes the fitness consequences of the parental age difference in ruffed lemurs
Proceedings of the Royal Society B: Biological Sciences . 285 ( 1886 ) : 20181479
Gearing up to handle the mosaic nature of life in the quest for orthologs
Bioinformatics . 34 ( 2 ) : 323-329
DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment
Environmental Science and Technology . 52 ( 24 ) : 14461-14468
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
Réseaux et connectivité
Prospectives de l’Institut Ecologie et environnement du CNRS : compte-rendu des journées des 22, 23 et 24 février 2017, CNRS, Bordeaux . : 187-193
MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps
Genome Biology and Evolution . 9 ( 10 ) : 2506-2509
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431