List

New "Mini-projets" started in 2017

Project Scientific supervisor Key words Collaborator Type
Inventaires v3 C. Houbin observation, inventaires FR2424 Dev
Chondrus_annot_v2 J. Collen IdeAlg, Genome, Chondrus, Genomique UMR7139 Bio
ChondrusDB_v2 J. Collen IdeAlg, Genome, Chondrus, Jbrowse/Apollo UMR7139 E-infra
Quercus J.-P. Mevy RNAseq de novo, Quercus, adaptation IMBE Bio
DuckLiver C. Diot RNAseq de novo, Canard, hybrides, adaptation INRA Saint Gilles Bio
Transition du système de management de la qualité en ISO9001 v2015 E. Corre ISO 9001:2015, qualité, certification ABiMS Mngt

 

"Mini-projets" 2016

Project Scientific supervisor Key words Collaborator Type
Site Web Formation C. Cabresin enseignement, site web, formulaire, drupal FR2424 E-infra
PhaeoNO E. Marechal RNA-seq CEA/UMR 5168 Bio
AM1 M. Jebhar assemblage genome archaea IUEM Bio
Artemia C. Lejeusne RNA-seq UMR7144 Bio
SIP-LIEC F. Thomas RNA-seq UMR8227 Bio
Heterotis J. Henry RNA-seq BOREA Caen Bio
Sacculine J. Henry RNA-seq BOREA Caen Bio
Meta-transcriptome Mucus Truite V. Cornet RNA-seq Univ. Namur Bio
CBM-DOI N. Guyard DOI, CBM FR2424 Dev
MucorDB2 J.L. Jany, L. Meslet Apollo, annotation experte, Mucor, champignon, fromage LUBEM (UBO) E-infra
Posidonie Y. Ferandin RNA-seq Banyuls Bio
AdaptSearch D. Jollivet Orthologues, detection, Galaxy UMR7144 E-infra
W4M_IPO Y. Guitton W4M,Galaxy LABERCA E-infra

 

"Mini-projets" 2015

Project Scientific supervisor Key words Collaborator Type
Caractérisation du biofilm formé dans les serres de production de tomates Roby Metabarcoding, MiSeq Vegenov Bio
SBEMET : Extraction et visualisation des données météo en temps réel Cariou hf, meteo, bdd, observation, web FR2424 Dev
Galaxy4SNiPlay V2 A. Dereeper SNP, diversity genetic, visualization, haplotypes, Galaxy CIRAD - Southgreen platform E-Infra
REPET Galaxy V2 O. Inizan transposable elements, REPET, Galaxy, IFB URGI Versailles - Genome Analysis

E-infra

Oasearch V2 D. Jollivet Orthologues, detection UMR7144 E-infra
SEPIOM L.Bonnaud Transcripome Sepia UMR Borea Paris Bio
Sepia V4 J. Henry C. Gaudin Transcripome Sepia UMR Borea Caen Bio
Labrax J. Henry C. Gaudin Transcripome Labrax UMR Borea Caen Bio
Pecten J. Henry C. Gaudin Transcripome Pecten UMR Borea Caen Bio
Pterois J. Henry C. Gaudin Transcripome Pterois UMR Borea Caen Bio
CALYpSO A.C. Baudoux Metavirome UMR7144 Bio
Polar Poux J.Y. Toullec M. Gonzalez Transcripome isopde UMR7144 - INACH Chili Bio
Polar Urchin J.Y. Toullec M. Gonzalez Transcripome urchin UMR7144 - INACH Chili Bio
Mucor J.L.Jany L.Cladiere Genome Mucor ESIAB-UBO Bio
MicroMar C. Jeanthon Transcriptome diatome UMR7144 Bio
Radiolaria F. Not Transcriptome radiolaire UMR7144 Bio
Tr_C.virginica B.Allam Transcriptome Stony Brook University, NY Bio
Tr_Diatom F. Vincent Transcriptome ENS Paris Bio
ectocarpus epibiont P. Potin Metabarcode UMR8227 Bio
StartCorrector L. Garczarek F. Partensky Cyanorak UMR7144 Dev
synProDB L. Garczarek F. Partensky jbrowse, synechococcus UMR7144 E-infra
Assemblage de génomes d'Archea S. Lharidon Assembly, ION Torrent, Illumina Univ Brest Bio
STAR F. Nunes rnaseq, met transcriptomique LEBAM/IFREMER Bio

 

"Mini-projets" 2014

Project Scientific supervisor Key words Collaborator Type
Renkan V2 F. Not   UMR7144 Dev
Inventaires V2 C. Houbin   FR2424 Dev
Wisca Galaxy G.Farrant Galaxy, scaffolding, genome UMR7144

E-infra

Galaxy4SNiPlay A. Dereeper SNP, diversity genetic, visualization, haplotypes, Galaxy CIRAD - Southgreen platform E-infra
Galaxy4Blast E. Corre Blast, workflow, uniq acces, authentification, visualization, automatisation FR2424 E-infra
Galaxy4Genomer G. Le Corguillé Archive, client link, Galaxy, data traitement, exportation FR2424 E-infra
SClims G. Michel Tool, web, history, gene, sequence UMR8227 Dev
Assemblage de génomes de Flavobactéries marines G. Michel Flavobactéries, MiSeq UMR8227 Bio
Tr_bivalves J. Henry   Univ Caen Bio
Tr_Tilapia J. Henry   Univ Caen Bio
REPET Galaxy O. Inizan transposable elements, REPET, Galaxy, IFB URGI Versailles - Genome Analysis E-infra
COLMAR P.J. Lopez Bio-constructions, Polychaetes, Annélides, Espèce ingénieur, Evolution UMR BOREA Bio
TransAlg V2 S. Dittami   URM8227 Bio
Workflow4Metabo_ThalassOMICS Y. Guitton Galaxy, Metabolomique, Workflow MMS EA2160 - ThalassOMICS E-infra
Galaxy4NMR G. Le Corguillé RMN / métabolomique / Analyse Statistique / Worflow / Galaxy CEISAM - UMR 6230 / SPCMIB - UMR 5068 E-infra
Oasearch D. Jollivet Orthologues, detection UMR7144 E-infra
Traductome V2 J. Morales polysomes, traductome, RNA-binding proteins, RNA-seq DE, Paracentrotus lividus UMR 8227 Bio
Photothèque SMO W. Thomas Photos, Vidéos, Diffusion, Organisation et Sécurité FR2424 E-infra
Poursuite de l’intégration des données HF dans le « HF data repository » Cariou Meteo data UMR7144 Dev
Mucoroscope J.L. Jany L. Meslet Analyse RNAseq LUBEM Bio
MucorDB J.L. Jany L. Meslet annotation, mucor, blast LUBEM E-infra
Radiolaria-symbiose F. Not - L. Bitner Transcriptome holobionte radiolaire UMR7144 - UPMC Bio

 

"Mini-projets" 2013

Project Scientific supervisor Key words Collaborator Type
Hectar V3 B. Gschloessl   CBGP INRA E-infra
GISM V2 L. Leveque sea trip, planning, workflows FR2424 Dev
galaxy4resomar I. Ghaillard galaxy, statistics, R RESOMAR E-infra
galaxy4metabarcoding S. Audic galaxy, metabarcoding, tara UMR7144 E-infra
InterEsil T. Tonon ectocarpus, transcriptomic, analysis, pipeline, galaxy UMR7139 E-infra
Ccarn J. collen chrondrus statistic analysis, red seaweeds, EST UMR7139 Bio
chondrusDB J. Collen chrondrus, data integration, RNA-seq, annotation UMR7139 E-infra
ectocarpusDB M. Cock ectocarpus, data integration, RNA-seq, annotation UMR7139 E-infra
Marine Model Organism DB C. Caron data integration, EMBRC, galaxy, marine genome EMBRC-France Dev
PhaeBact T. Tonon abiotic stress, functional genomic, macroseaweeds UMR7139 Bio
SulfAtlas G. Michel polysaccharides, sulfatases, bacteria, seaweeds UMR7139 Dev
Ectocarpus shoremap S. Coelho     Bio
Ectocarpus sexseaweed S. Coelho     Bio
Proteome discover Delage Analyse, protéomique UMR8227 Bio
Sepia theb J. Henry   Univ Caen Bio
Pleurodèles J.Y. Sire   Univ Caen Bio
WiseScaffolder G. Farrant   UMR7144 Dev
SALGENE P.J. Lopez   UMR BOREA Bio
Workflow4MetaboCorsaire A. Gravot Galaxy, Métabolomique, workflow, xcms, statistiques, Drupal Univ Rennes - P2M2 E-infra
Mercenaria RNAseq B. Allam   Stony Brook University, NY Bio
Analyse seq ADN S. Dumanoir modèles pré-cliniques, mutations, sélection IRCM - INSERM U896 E-infra
myTrash C. Caron   FR2424 E-infra

 

"Mini-projets" 2012

Project Scientific supervisor Key words Collaborator Type
CBM V2 D. Davoult / N. Guyard marine biological notebook, publications, archiving FR2424 Dev
ectoTilling M. Cock mapping, SNP, UMR7139

Bio

RmetaT MJ Delmas (meta)-transcriptomic, pico eukaryotes, cocolithophore, assembly, Tara. UMR7144/ EPPO Bio
TransAlg T. Tonon   UMR 7139 / IDEALG Bio
Reprosep J. Henry Sepia, Penaeus vannamei , RNASeq, main nervous system, reproduction

CNRS INEE FRE 3484 BioMEA / Université de Caen

Bio
Esil SNP Mark Cock Ectocarpus, SNP UMR 7139 Bio
uORF2 Julia Morales   UMR 7150 Bio
IsochrysisI M. Garnier, B. Saint-Jean transcriptomic , RNAseq IFREMER Nantes Bio
IsochrysisK M. Garnier, B. Saint-Jean transcriptomic , RNAseq IFREMER Nantes Bio
Etude de la flore totale de l’éponge
Asbestopluma hypogea
S. Dupont metagenomic MNHN Bio
Comparaison des séquences et des
activités enzymatiques des désaturases
FADS1 et FADS2
S. Mazan pipeline, protein, family UMR 7150 / UMR 7139 / IFREMER Bio

Scyliorhinus canicula genome project

S. Mazan Annotation, genome, transcriptome

UMR7150

consortium GenoShark

Bio
Annotation d'un transcriptome
de mâchoire de crocodile
Jean-Yves Sire annotation, transcriptome UMR7138 / UPMC Bio
Analyses Phylogénétiques des familles de
protéines CDK et Cyclines
P. Colas phylogeny USR3151 Bio
ARRAYSyn L. Garczarek picocyanobacteria, "puce à ADN", Bioconductor UMR7144 Bio
e-infrastructure metrology C. Caron metrology, flow analysis, optimization FR 2424 Dev
Cahiers de Biologie Marine V2 D. Davoult marine biological notebook, publications FR 2424 Dev
Renkan F. Not collection, plancton, protist UMR7144 Dev
GISM V1 L. Leveque sea trip, planification, workflows FR2424 Dev
Inventaire C. Houbin   FR2424 Dev

 

"Mini-projets" 2011

Project Scientific supervisor Key words Collaborator Type
RNA Seq Laminaria Lessonia Catherine Leblanc RNAseq, brown algae, L. digitata, L. nigressens, Herbivory UMR 7139 Bio
RNAseq Bathymodiolus azoricus Arnaud Tanguy RNAseq, mollus UMR 7144 Bio
Criblage du facteur de régulation 4E-interacting protein chez les cnidaires Julia Morales Sea urchin, cnidaires, regulation,transcription UMR 7150 Bio
ATK - Polysomes P. lividus Julia Morales Sea urchin ,traductome UMR 7150 Bio
Analyse transcriptomique virus vs Emiliana huxleyi Colomban de Vargas Viral infection, micro-arrays, coccolithophores foraminifers UMR 7144 Bio
Ectobacter Thierry Tonon phylogeny, blast, Ectocarpus UMR 7139 Bio
IMM-ORO array experiment Mark Cock Life cycle regulation, brown algae, mutant, transcriptomic, micro-arrays UMR 7139 Bio
RNASeq Ectocarpus Susana Coehlo RNAseq, brown algae, transcriptomic, sexual differentiation UMR 7139 Bio
Euphausia Jean-Yves Toullec RNAseq, Euphosia crystallorophias, temperature effect, kril UMR 7144 Bio
Upstream ORF search on urchin genome Julia Morales µORF, screening, Expression regulation, UMR 7150 Bio
RNAseq Perkinsus marinus B. Allam, Stony Brook RNAseq , parasite , oyster, Perkinsus marinus

UMR 7144

University. NY. USA

Bio
SSR Serpula lacrymans Gaetan Le Floch SSR screening, biodiversity, microbial ecology ESMISAB Brest Bio
I² (Inventaires x Images) Céline Houbin flore et faune marine, inventaire, bases de données, images FR 2424 Dev
RENKAN Fabrice Not sample database, images, web interface UMR 7144 Dev
Portail outils Christophe Caron tools, platform, directory, database FR 2424 Dev
Cahiers de Biologie Marine D. Davoult marine biology, web, database, review FR 2424 Dev
Formulaire accueil scientifique Cécile Cabresin workflow, accueil scientifique, ASSEMBLE FR 2424 Dev

 

"Mini-projets" 2010

Project Scientific supervisor Key words Collaborator Type
P. lividus polysome transcriptome Julia Morales RNAseq, sea urchin UMR 7150 Bio
FerryBox Database Pascal Morin ferry, transect, database, physical/chemical parameters UMR 7144 Dev
Chondrus crispus genome annotation

Catherine Boyen / Jonas Collen

Full genome , genetic model, annotation,.red algae UMR 7139 & consortium Bio
Picoeucaryotes Daniel Vaulot diversity analysis, metagenome, NGS, flow cytometry sorting, picoplancton UMR 7144 Bio

 

Accomplished projects

  • CapExBio (2008-2010)
  • MIGADI (2008-2010)
    • This project aims at developping an innovating bioinformatic environment dedicated to genome annotation and microbial proteom. It is based on current resources from both ABiMS and MIGALE platforms, and on several research programs from the MIG (MOSAIC) and MIA-J (PARIS) units. The integration process is based on the deployment of web service technologies. This project was financed by the ANR PTFV 2007. An oral presentation (Web Services for MIcrobial Genome Annotation using Data Integration) was given in 2010 at the JOBIM convention.