Computing services
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Ingénieur d'études
CNRS
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CNRS
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Technicien
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CNRS
Tel: 33 04 72 44 85 44
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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 61 to 90 publications on 167 in total
Réseaux et connectivité
Prospectives de l’Institut Écologie et environnement du CNRS . : 187-193
Book chapter
see the publicationAncestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431
DOI: 10.1093/gbe/evx255
Journal article
see the publicationMaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
DOI: 10.1101/127548
Other publication
see the publicationFruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies
The American Naturalist . 188 ( 1 ) : 66-75
DOI: 10.1086/686684
Journal article
see the publicationInferring the timing of territoriality and rut in male roe deer from movements?
8. EURODEER meeting .
Conference paper
see the publicationColib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
GigaScience . 5 ( 1 )
Journal article
see the publicationQuantitative Molecular Detection of 19 Major Pathogens in the Interdental Biofilm of Periodontally Healthy Young Adults
Frontiers in Microbiology . 7 : 840 - 840
Journal article
see the publicationHow Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience
PLoS Biology . 14 ( 8 ) : e1002527
Journal article
see the publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Journal article
see the publicationSNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
Nucleic Acids Research .
DOI: 10.1093/nar/gkw655
Journal article
see the publicationNo Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes
Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620
Journal article
see the publicationRAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements
Nucleic Acids Research . 43 ( 10 ) : 4833--4854
DOI: 10.1093/nar/gkv370
Journal article
see the publicationDNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity
PLoS ONE . 10 : e0129427
Journal article
see the publicationUnknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions.
Epidemics . 11 : 48-55
Journal article
see the publicationOptimization of multiplexed RADseq libraries using low-cost adaptors
Genetica . 143 ( 2 ) : 139-143
Journal article
see the publicationDetermining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method
European Journal of Entomology . 111 ( 4 ) : 567-573
Journal article
see the publicationHost plant specialization matters in the epidemiology of Wolbachia across phytophagous wasps (Hymenoptera: Torymidae)
8. International Wolbachia Conference . : np
Poster
see the publicationSpatially constrained clustering of ecological networks
Methods in Ecology and Evolution . 5 ( 8 ) : 771-779
Journal article
see the publicationFast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles
Lecture Notes in Computer Science . 8452 : 248-258
Journal article
see the publicationStatistical handling of reproduction data for exposure-response modeling
Environmental Science and Technology . 48 : 7544-51
DOI: 10.1021/es502009r
Journal article
see the publicationNavigating in a Sea of Repeats in RNA-seq without Drowning
WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96
Conference paper
see the publicationEpidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters.
Molecular Ecology Notes . 23 ( 9 ) : 2362-2375
DOI: 10.1111/mec.12737
Journal article
see the publicationThe 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
Journal article
see the publicationNew 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 paper
see the publicationConference Report: Deuxièmes Rencontres R
The R Journal . 5/2 : 164--165
Journal article
see the publicationFast 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.
Conference paper
see the publicationToward community standards in the quest for orthologs
Bioinformatics . 28 ( 6 ) : 900-904
Journal article
see the publicationGenome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate
Journal of Bacteriology . 194 ( 24 ) : 6939-6939
DOI: 10.1128/JB.01856-12
Journal article
see the publication