Tel: 33 04 72 43 11 68
Tel: 04 72 43 35 82
Tel: 33 04 72 43 29 04
Ingénieur de recherche
Tel: 33 04 72 44 85 44
Tel: 04 72 44 81 42
Tel: 33 04 72 43 29 04
Tel: 33 04 72 44 85 98
Ingénieur de recherche
Tel: 33 04 72 43 29 07
Ingénieur de recherche
Tel: 33 04 26 23 44 70
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.
Software and methodological development
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 61 to 90 publications on 156 in total
Calcul parallèle avec R
Booksee the publication
RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements
Nucleic Acids Research . 43 ( 10 ) : 4833--4854
DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity
PLoS ONE . 10 : e0129427
Unknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions.
Epidemics . 11 : 48-55
Optimization of multiplexed RADseq libraries using low-cost adaptors
Genetica . 143 ( 2 ) : 139-143
Determining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method
European Journal of Entomology . 111 ( 4 ) : 567-573
Host plant specialization matters in the epidemiology of Wolbachia across phytophagous wasps (Hymenoptera: Torymidae)
8. International Wolbachia Conference . : np
Postersee the publication
Spatially constrained clustering of ecological networks
Methods in Ecology and Evolution . 5 ( 8 ) : 771-779
Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles
Lecture Notes in Computer Science . 8452 : 248-258
Statistical handling of reproduction data for exposure-response modeling
Environmental Science and Technology . 48 : 7544-51
Navigating in a Sea of Repeats in RNA-seq without Drowning
WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96
Epidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters.
Molecular Ecology Notes . 23 ( 9 ) : 2362-2375
L'ADN, mémoire numérique du vivant
Pour la science . : 102-108
The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle.
Molecular Biology and Evolution . 30 ( 2 ) : 369-83
New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .
Conference Report: Deuxièmes Rencontres R
The R Journal . 5/2 : 164--165
Fast and parallel algorithm for population-based segmentation of copy-number profiles
10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) . 8452 : 275 p.
Toward community standards in the quest for orthologs
Bioinformatics . 28 ( 6 ) : 900-904
Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate
Journal of Bacteriology . 194 ( 24 ) : 6939-6939
BioNLP Shared Task - The Bacteria Track
BMC Bioinformatics . 13 : np
Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
Heredity . 108 ( 3 ) : 285-291
An evaluation of the effects of Lactobacillus ingluviei on body weight, the intestinal microbiome and metabolism in mice
Microbial Pathogenesis . 52 ( 1 ) : 61-68
The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis
PLoS ONE . 7 ( 2 ) : e31490
High-quality sequence clustering guided by network topology and multiple alignment likelihood.
Bioinformatics . 28 ( 8 ) : 1078-85
RENABI GRISBI Infrastructure Distribuée pour la Bioinformatique
JOBIM 2011 - Journées Ouvertes Biologie Informatique Mathématique .
PhEVER: a database for the global exploration of virus-host evolutionary relationships.
Nucleic Acids Research . 39 ( Database issue ) : D569-75
Orientia tsutsugamushi Stimulates an Original Gene Expression Program in Monocytes: Relationship with Gene Expression in Patients with Scrub Typhus
PLoS Neglected Tropical Diseases . 5 ( 5 ) : e1028
Genetic structure and linkage disequilibrium in 4 Vitis species
Plant and Animal Genomes Conference . : np
Ultra-fast sequence clustering from similarity networks with SiLiX
BMC Bioinformatics . 12(116) : 1-9
BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming
Proceedings of the BioNLP Shared Task 2011 ACL Workshop . 13 9781937284091 : 65-73