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 121 to 150 publications on 153 in total

Path-equivalent developments in acyclic weighted automata

Mathieu Giraud, Philippe Veber, Dominique Lavenier

International Journal of Foundations of Computer Science . 18 ( 4 ) : 799-812

DOI: 10.1142/S012905410700498X

Journal article

see the publication

Qualitative, integrated modeling of lipid metabolism in hepatocytes

O Radulescu, A Siegel, Mathieu Le Borgne, Philippe Veber, E Pécou, Sandrine Lagarrigue...

7th International Conference on Systems Biology - Yokohama . : Inconnu

Poster

see the publication

Topology and static response of interaction networks in molecular biology

Ovidiu Radulescu, Sandrine Lagarrigue, Anne Siegel, Philippe Veber, Michel Le Borgne

Journal of the Royal Society Interface . 3 ( 6 ) : 185 - 196

DOI: 10.1098/rsif.2005.0092

Journal article

see the publication

Lagrangian Approaches for a class of Matching Problems in Computational Biology

Nicola Yanev, Rumen Andonov, Philippe Veber, Stefan Balev

Report

see the publication

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks

Anne Siegel, Ovidiu Radulescu, Michel Le Borgne, Philippe Veber, Julien Ouy, Sandrine Lagarrigue

BioSystems . 84 : 153-174

Journal article

see the publication

Lagrangian Approaches for a class of Matching Problems in Computational Biology

Nicola Yanev, Rumen Andonov, Philippe Veber, Stefan Balev

: 18

Report

see the publication

ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis

Adil El Filali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot

Nucleic Acids Research . 34 ( 90001 ) : D613-D616

DOI: 10.1093/nar/gkj022

Journal article

see the publication

Path-Equivalent Removal of Epsilon-Transitions

Dominique Lavenier, Philippe Veber, Mathieu Giraud

11th International Conference on Implementation and Application of Automata (CIAA 2006) . : 23--33

DOI: 10.1007/11812128_4

Conference paper

see the publication

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Jean-François Dufayard, L. Duret, Simon Penel, Manolo Gouy, F. Rechenmann, G. Perrière

Bioinformatics . 21 ( 11 ) : 2596-603

DOI: 10.1093/bioinformatics/bti325

Journal article

see the publication

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz...

Nucleic Acids Research . 33 ( Database issue ) : D297-302

DOI: 10.1093/nar/gki039

Journal article

see the publication

Complex Qualitative Models in Biology: a new approach

Philippe Veber, Michel Le Borgne, Anne Siegel, Sandrine Lagarrigue, Ovidiu Radulescu

Complexus . 2 : 140-151

Journal article

see the publication

Polymorphix: a sequence polymorphism database

E. Bazin, L. Duret, Simon Penel, N. Galtier

Nucleic Acids Research . 33 : 481-484

Journal article

see the publication

Projet MERLIN 2005

Benoit Chassigneux, Stéphane Pouyllau, Julien Barnier, Armelle Toulemonde

Le Journal du CNRS .

Journal article

see the publication

Data Documentation Initiative : traduction française de la version 1.2.2

Julien Barnier, Jean Noel Bouvier, Carine Lecerf, Christine Maury, Jean-Philippe Talec

Other publication

see the publication

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Marie-Françoise Cochet, Philippe Veber...

Nucleic Acids Research . 32 ( 1 ) : 17-24

DOI: 10.1093/nar/gkg928

Journal article

see the publication

YodA from Escherichia coli is a metal-binding lipocalin-like protein

G. David, K. Blondeau, M. Schiltz, Simon Penel, A. Lewit-Bentley

Journal of Biological Chemistry . 278 : 43728-43735

Journal article

see the publication

Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings

Simon Penel, R.G. Morrison, P.D. Dobson, R.J. Mortishire-Smith, A.J. Doig

Protein Engineering . 16 : 957-961

Journal article

see the publication

Combinatorial approaches for segmentingbacterium genomes

Rumen Andonov, Nicola Yanev, Dominique Lavenier, Philippe Veber

Report

see the publication

Integrated databanks access and sequence/structure analysis services at the PBIL.

G. Perriere, C. Combet, Simon Penel, Christophe Blanchet, J. Thioulouse, C. Geourjon...

Nucleic Acids Research . 31 ( 13 ) : 3393-3399

DOI: 10.1093/nar/gkg530

Journal article

see the publication

Cartographie génomique comparée chez les mammifères

G. Bronner, B. Spataro, Christian Gautier

Médecine/Sciences . 18 : 767-774

Journal article

see the publication

Comparative genomic mapping in mammals

G. Bronner, B. Spataro, Christian Gautier

Médecine/Sciences . 18 : 767-774

Journal article

see the publication

Modeling comparative mapping using objects and associations

G. Bronner, B. Spataro, M. Page, Christian Gautier, F. Rechenmann

Computers and Chemistry . 26 : 413-420

Journal article

see the publication

Rotamer strain energy in protein helices - quantification of a major force opposing protein folding

Simon Penel, A.J. Doig

Journal of Molecular Biology . 305 : 961-968

Journal article

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Effect of the N1 residue on the stability of the alpha-helix for all 20 amino acids

D.A.E. Cochran, Simon Penel, A.J. Doig

Protein Science . 10 : 463-470

Journal article

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Stabilizing nonpolar/polar side-chain interactions in the alpha-helix

C.D. Andrew, Simon Penel, G.R. Jones, A.J. Doig

PROTEINS-STRUCTURE FUNCTION AND GENETICS . 45 : 449-455

Journal article

see the publication

Structure stability and folding of the alpha-helix

A.J. Doig, C.D. Andrew, D.A. Cochran, E. Hughes, Simon Penel, J.K. Sun...

Biochemical Society Symposia . 68 : 95-110

Journal article

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GeMME une interface modélisant la cartographie comparée des mammifères Application

B. Spataro

incollection . -- : 333-340

Journal article

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Determination of alpha-helix N1 energies after addition of N1 N2 and N3 preferences to helix/coil theory

J.K. Sun, Simon Penel, A.J. Doig

Protein Science . 9 : 750-754

Journal article

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Periodicity in alpha-helix lengths and C-capping preferences

Simon Penel, R.G. Morrison, R.J. Mortishire-Smith, A.J. Doig

Journal of Molecular Biology . 293 : 1211-1219

Journal article

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Side-chain structures in the first turn of the alpha-helix

Simon Penel, E. Hughes, A.J. Doig

Journal of Molecular Biology . 287 : 127-143

Journal article

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