Computing services

Members

 

info@listes-lbbe.univ-lyon1.fr

 

 

The "Pôle informatique" (hereafter called "PI") is constituted of 9 engineers (1T, 5IE, 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.
Cluster de calcul UMR5558/PRABI
  • Compute and storage: since 2009, the PI manages a computing cluster with almost 1200 avalaible computing cores. The cluster is linked to a 600 TB high performing distributed storage system under BeeGFS and an object mode storage based on iRods (~400 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 91 to 120 publications on 153 in total

The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis

Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib...

PLoS ONE . 7 ( 2 ) : e31490

DOI: 10.1371/journal.pone.0031490

Journal article

see the publication

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

see the publication

RENABI GRISBI Infrastructure Distribuée pour la Bioinformatique

Christophe Blanchet, Clément Gauthey, Christophe C. Caron, Olivier Collin, Stephane Delmotte, Tiphaine Martin...

JOBIM 2011 - Journées Ouvertes Biologie Informatique Mathématique .

Conference paper

see the publication

PhEVER: a database for the global exploration of virus-host evolutionary relationships.

Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, Christian Gautier

Nucleic Acids Research . 39 ( Database issue ) : D569-75

DOI: 10.1093/nar/gkq1013

Journal article

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Orientia tsutsugamushi Stimulates an Original Gene Expression Program in Monocytes: Relationship with Gene Expression in Patients with Scrub Typhus

Wiwit Tantibhedhyangkul, Thanavadee Prachason, Duangdao Waywa, Adil El Filali, Eric Ghigo, Wanna Thongnoppakhun...

PLoS Neglected Tropical Diseases . 5 ( 5 ) : e1028

DOI: 10.1371/journal.pntd.0001028

Journal article

see the publication

Genetic structure and linkage disequilibrium in 4 Vitis species

Patrice This, Stephane Nicolas, Jean-Pierre Peros, Thierry Lacombe, Loic Le Cunff, Jean-Michel Boursiquot...

Plant and Animal Genomes Conference . : np

Conference paper

see the publication

BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming

Julien Jourde, Alain-Pierre Manine, Philippe Veber, Karen Fort, Robert Bossy, Erick Alphonse...

Proceedings of the BioNLP Shared Task 2011 ACL Workshop . 13 9781937284091 : 65-73

Conference paper

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Utilisation de grilles de calcul pour la génomique comparative

Simon Penel, Christophe Blanchet, Pascal Calvat, Yonny Cardenas, Clement Gauthey, Jean Yves Nief...

Rencontres Scientifiques France Grilles 2011 .

Conference paper

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ReNaBi-GRISBI: grande infrastructure pour la bioinformatique

Christophe Blanchet, Clément Gauthey, Olivier Collin, Tiphaine Martin, Nouredine Melab, Frederic Plewniak...

JOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques .

Conference paper

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Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming

Martin Gebser, Carito Guziolowski, Mihail Ivanchev, Torsten Schaub, Anne Siegel, Philippe Veber...

Principles of Knowledge Representation and Reasoning .

Conference paper

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Genetic structure and linkage disequilibrium in 4 Vitis species

Stephane Nicolas, Jean-Pierre Peros, Patrice P. This, Thierry Lacombe, Valerie V. Laucou, Loic L. Le Cunff...

Grapevine breeding and genetics .

Poster

see the publication

Genetic structure and linkage disequilibrium in four Vitis species

Stephane Nicolas, Jean-Pierre Peros, Patrice P. This, Thierry Lacombe, L. Le Cunff, Jean-Michel Boursiquot...

10. International Conference on Grapevine Breeding and Genetics .

Conference paper

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Genetic structure and linkage disequilibrium in 4 species of the Vitis genus

Patrice P. This, Stephane Nicolas, Alexis Dereeper, Agnès Doligez, Jean-Pierre Peros, Roberto Bacilieri...

Génoplante .

Poster

see the publication

VirHostNet : a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks

Vincent Navratil, Benoit de Chassey, Laurène Meyniel, Stephane Delmotte, Christian Gautier, Patrice André...

Nucleic Acids Research . 37 : D661-D668

DOI: 10.1093/nar/gkn794

Journal article

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Databases of Homologous Gene Families for Comparative Genomics

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, L. Duret...

BMC Bioinformatics . 10 (Suppl.6) :S3 : 13

DOI: 10.1186/1471-2105-10-S6-S3

Journal article

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DigiPINS: A database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies

Vincent Navratil, Simon Penel, Stephane Delmotte, Dominique Mouchiroud, Christian Gautier, Abdel Aouacheria

Biochimie . 90 ( 4 ) : 563-569

DOI: 10.1016/j.biochi.2007.09.017

Journal article

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DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies.

V. Navratil, Simon Penel, Sebastien Delmotte, D. Mouchiroud, Christian Gautier, A. Aouacheria

Biochimie . xxx : 563-569

Journal article

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Lagrangian approaches for a class of matching problems in computational biology

Nicola Yanev, Rumen Andonov, Philippe Veber, Stefan Balev

Computers & Mathematics with Applications . 55 ( Issue 5 (March 2008) ) : 1054-1067

DOI: 10.1016/j.camwa.2006.12.103

Journal article

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Inferring the role of transcription factors in regulatory networks

Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel

BMC Bioinformatics . 9 : nc

DOI: 10.1186/1471-2105-9-228

Journal article

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Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A. Studer, Simon Penel, L. Duret, M. Robinson-Rechavi

Genome Research . 18 : 1393-1402

Journal article

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Détection de domaines dans des séquences génomiques : un problème de couverture optimale

Philippe Veber, Sébastien Tempel, Rumen Andonov, Dominique Lavenier, Jacques Nicolas

FRANCORO V/ROADEF 2007 .

Conference paper

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Decision Diagrams for Qualitative Biological Models

Michel Le Borgne, Philippe Veber

: 17

Report

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Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study

Carito Guziolowski, Philippe Veber, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel

: 14

Report

see the publication

Inferring the role of transcription factors in regulatory networks

Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel

Report

see the publication

Optimiser un plan d'expérience à partir de modèles qualitatifs?

Anne Siegel, Carito Guziolowski, Philippe Veber, Ovidiu Radulescu, Michel Le Borgne

Biofutur . 275 : 27-31

Journal article

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Modélisation grande échelle de réseaux biologiques : vérification par contraintes booléennes de la cohérence des données

Philippe Veber

Thesis

see the publication

Qualitative response of interaction networks: application to the validation of biological models

Anne Siegel, Carito Guziolowski, Philippe Veber, Ovidiu Radulescu, Michel Le Borgne

6th International Congress on Industrial and Applied Mathematics. ICIAM 07 . : nc

Conference paper

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Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study

Carito Guziolowski, Philippe Veber, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel

Journal of Biological Physics and Chemistry . 7 : 37-43

Journal article

see the publication