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 121 to 143 publications on 143 in total
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
Bioinformatics . 21 ( 11 ) : 2596-603
Polymorphix: a sequence polymorphism database
Nucleic Acids Research . 33 : 481-484
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Nucleic Acids Research . 33 ( Database issue ) : D297-302
seq++: a package for biological sequences analysis with a range of Markov-related models
Bioinformatics . 21 : 2783-2784
GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.
Nucleic Acids Research . 32 ( 1 ) : 17-24
Combinatorial approaches for segmentingbacterium genomes
Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings
Protein Engineering . 16 : 957-961
YodA from Escherichia coli is a metal-binding lipocalin-like protein
Journal of Biological Chemistry . 278 : 43728-43735
Integrated databanks access and sequence/structure analysis services at the PBIL.
Nucleic Acids Research . 31 ( 13 ) : 3393-3399
Comparative genomic mapping in mammals
médecine/sciences . 18 : 767-774
Modeling comparative mapping using objects and associations
Computers and Chemistry . 26 : 413-420
Cartographie génomique comparée chez les mammifères
médecine/sciences . 18 : 767-774
GeMME une interface modélisant la cartographie comparée des mammifères Application
incollection . -- : 333-340
Stabilizing nonpolar/polar side-chain interactions in the alpha-helix
PROTEINS-STRUCTURE FUNCTION AND GENETICS . 45 : 449-455
Structure stability and folding of the alpha-helix
Biochemical Society Symposia . 68 : 95-110
Rotamer strain energy in protein helices - quantification of a major force opposing protein folding
Journal of Molecular Biology . 305 : 961-968
Effect of the N1 residue on the stability of the alpha-helix for all 20 amino acids
Protein Science . 10 : 463-470
Determination of alpha-helix N1 energies after addition of N1 N2 and N3 preferences to helix/coil theory
Protein Science . 9 : 750-754
Periodicity in alpha-helix lengths and C-capping preferences
Journal of Molecular Biology . 293 : 1211-1219
Side-chain structures in the first turn of the alpha-helix
Journal of Molecular Biology . 287 : 127-143
Detergent binding in trigonal crystals of OmpF porin from Escherichia coli
Biochimie . 80 : 543-551
Neutron crystallographic evidence of lipase-colipase complex activation by a micelle
EMBO Journal . 16 : 5531-5536
MAINDEX - manual indexation for area-detector crystallographic data
Journal of Applied Crystallography . 30 : 206-206