ABiMS

Adress
Place Georges Teissier - Station Biologique de Roscoff 29680 Roscoff
Structure(s)
CNRS
Unit:
FR2424
Regional Center
IFB West
Website
Roscoff
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • ISO 9001
Infrastructure
Propriétaire
Effective storage
800.00 To
Cluster: cores number
2 000 cores
CPU/hours a year
2 300 000 H / an
Bioinformatic tools number
400
Users number (last year)
500
Servers description
  • Database server : MysQL + PostreSQL
  • Biotsta R server
  • Web servers
  • Galaxy production servers : NGS, Metabolomics et Public
  • Galaxy development server
  • 56 cluster nodes
  •  master node
  • 4 NFS servers

No website documented
Annual visits:
Not documented
Unique visits:
400 an
Quotes:
Not documented
Downloads:
Not documented

Galaxy

Description
Access conditions

http://galaxy.sb-roscoff.fr/

No website documented
Annual visits:
Not documented
Unique visits:
100 an
Quotes:
Not documented
Downloads:
Not documented

Workflow4Metabolomics

Description
Access conditions

http://workflow4metabolomics.org/

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

MicRhoDE workflow

Description

MicRhoDE workflow: places query sequences into MicRhoDE tree (type-1 rhodopsin phylogeny). [webpage]

Access conditions

http://webtools.sb-roscoff.fr : Galaxy instance that host tools developped at the Station Biologique de Roscoff in collaboration with ABiMS (no account)

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

WiseScaffolder

Description

WiseScaffolder: genome scaffolding of pre-assembled contigs using mate-pair data. [webpage]

Access conditions

http://webtools.sb-roscoff.fr : Galaxy instance that host tools developped at the Station Biologique de Roscoff in collaboration with ABiMS (no account)

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

HECTAR

Description

Hectar: Predict subcellular targeting for heterokont proteins. 

Access conditions

http://webtools.sb-roscoff.fr : Galaxy instance that host tools developped at the Station Biologique de Roscoff in collaboration with ABiMS (no account).

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

JBrowse / WebApollo browsers

Description

Genome browser sfor marine model organsims 

Access conditions

MMODB Acces : EMBRC France

Domains of activity
  • Environment
  • Biology
  • Agri-food
Description of expertise domains

ABiMS works with research team within the framework of scientific collaboration formalised as project.

ABiMS provide differents services :

  • A scientific computing environment (Infrastructure As A Service - IAAS)
  • Advice and expertise in 'omic data analysis
  • Software engineering (information system, databases, ...)
  • User support and training
Keywords:
  • NGS data analysis
  • Methodology
  • Genome and transcriptome assembly
  • Read mapping
  • Genomics (DNA-seq)
  • Genome analysis
  • Structural and functional genome annotation
  • Transcriptomics (RNA-seq)
  • Differential gene expression analysis
  • Transcripts and transcript variants analysis
  • Variant calling
  • Analysis of gene expression regulation
  • Metagenomics, metatranscriptomics
  • Data curation
  • Tools
  • Tool integration
  • Interoperability
  • Interfaces, web portals
  • Workflows developments
  • Data
  • Data integration
  • Databases and information systems
  • Computing environments
  • Cluster
  • GPU
  • Molecular evolution
  • Genes and genomes
  • Selection detection
  • Comparative genomics
  • Genome comparison
  • Genomics: Chips
  • DNA chips
  • Functionnal
  • RNA chips
  • Expression
  • Metabolomics and fluxomics

Formation professionnelle

No website documented
Trainees:
261 trainees / year
Training time:
Not documented
No upcoming session scheduled

Formation ABiMS

Description

L'offre de formation repose sur des modules de formation d'initiation aux environnements (Linux, Cluster, etc.), d'utilisation des outils (Galaxy, etc.) et langages (PERL, R, etc.), et de compréhension des méthodes (RNA-seq, Analyses statistiques, etc.). ABiMS est également en mesure de proposer des formations à façon pour des communautés (e.g. Métabolomique) ou des projets (École thématique).
Universitaires.

 

  • Galaxy pour l'analyse de données métabolomique (1 jour)
  • Cluster (1 jour)
  • Linux Initiation (1 jour)
  • Linux avancé (1 jour)
  • Linux scripting (1 jour)
  • Galaxy initiation (1 jour)
  • Galaxy RNAseq de novo/avec référence & cleaning (2 jours)
  • Galaxy : initiation à la phylogénie (2 jours)
  • R initiation (1 jour)
  • R avancé (1 jour)
Access conditions

Ouvert à tous avec facturation

No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

Cluster

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

Linux initiation

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

Linux avancé

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

R initiation

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

R avancé

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
1 day(s) / year
No upcoming session scheduled

Galaxy initiation

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
2 day(s) / year
No upcoming session scheduled

Galaxy : RNAseq de novo/avec référence & cleaning

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
2 day(s) / year
No upcoming session scheduled

Galaxy : Initiation à la phylogénie

Description
Not documented
Access conditions
Not documented
Users distribution
International
10 %
National
40 %
Regional
20 %
Local
30%
Explanation about this distribution:
Not documented
Platform's own projects

Not Documented

Collaborations
National projets
(10)
  • PIA IdealG 2011-2019
  • PIA OCEANOMICS 2012-2019
  • PIA EMBRC-France 2011-2019
  • ANR IMPEKAB 2015-2018
  • ANR HAPAR 2014-2019
  • ANR SAMOSA 2014-2017
  • ANR CALYpSO 2016-2017
  • ANR VIBRIOGEN 2011-2015
  • ANR ISOBAR 2014-2015
  • ANR SEXSEAWEED 2013-2016
International and European projects
(7)
  • ERC StG SEXSEA (susana COELHO) H2020 2015 : Origin and evolution of the sexes and reproductive systems: novel insights from a distant eukaryotic lineage
  • INFRADEV-4 EMBRIC (European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy)
  • INTEREG : ChanneLIS :  Channel Library and Information Services and is a project that will bring closer together library resources from SBR and MBA, on both sides of the Channel 
  • INTEREG : MARINEXUS  our shared seas - Mechanisms of ecosystem change in the Western Channel
  • MaCuMBA, Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications 
  • EMBRC :  ESFRI European Research Infrastructure – European Marine Biological Resource Centre
  • ASSEMBLE :  Association of European Marine Biological Laboratories
Projets with industry
(1)

Koriplast2 : programme de recherche collaboratif KoriPlast2 mené par Korilog, l’INRIA de Rennes et ABiMS ,  financé par la Région Bretagne et accompagné par le CRITT Santé Bretagne. 

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Animation du Groupe de travail Galaxy IFB

 

Mise en place de formation : Galaxy4Bioinformatics

 

(co)organisation des écoles/actions nationales AVIESAN, Galaxy4Bioinformatics, Workflow4Metabolomics

Internal publications

Workflow4Metabolomics: A collaborative research infrastructure forin computational metabolomics
Franck Giacomoni,†, Gildas Le Corguillé,†, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot, Christophe Caron. 2014, Bioinformatics, doi: 10.1093/bioinformatics/btu813

External publications

Dupont, Samuel; Corre, Erwan; Li, Yanyan; Vacelet, Jean; Bourguet-Kondracki, Marie-Lise. 2013. First insights into the microbiome of a carnivorous sponge. FEMS Microbiol Ecol. 2013 Jul 12. doi: 10.1111/1574-6941.12178.


G. Carrier, M. Garnier, L. Le Cunff, G. Bougaran, I. Probert, C. de Vargas, E. Corre, J.-P. Cadoret, and B. Saint-Jean, “Comparative Transcriptome of Wild Type and Selected Strains of the Microalgae Tisochrysis lutea Provides Insights into the Genetic Basis, Lipid Metabolism and the Life Cycle.,” PLoS ONE, vol. 9, no. 1, p. e86889, 2014.


Robert, M., Zatylny-Gaudin, C., Fournier, V., Corre, E., Le Corguillé, G., Bernay, B., & Henry, J. (2014). Transcriptomic and peptidomic analysis of protein hydrolysates from the white shrimp (L. vannamei). Journal of Biotechnology, 186C, 30–37. doi:10.1016/j.jbiotec.2014.06.020


Emmanuelle Pales Espinosa, Erwan Corre and Bassem Allam. 2014. Pallial mucus of the oyster Crassostrea virginica regulates the expression of putative virulence genes of its pathogen Perkinsus marinus. International Journal for Parasitology, 44(5), 305–317. doi:10.1016/j.ijpara.2014.01.006


Céline Zatylny-Gaudin Valerie Cornet; Joël Henry; Erwan Corre; Gildas Le Corguille; Bruno Zanuttin. 2014. Dual role of the cuttlefish salivary proteome in defense and predation ». Journal of Proteomics, 108, 209–222. doi:10.1016/j.jprot.2014.05.019.


Marie Robert, Céline Zatylny-Gaudin,Vincent Fournier, Erwan Corre, Gildas Le Corguillé ,Benoît Bernay, Joel Henry. Molecular and functional characterization of peptide fractions of a Tilapia (Oreochromis niloticus) by-product hydrolysate. Process Biochemistry, Volume 50, Issue 3, March 2015, Pages 487-492


V. Cornet, B.Houyvet, J.Henry, , B.Bernay, E.Corre, G. Le Corguillé, C. Zatylny-Gaudin. The Toll/NF-<kappa>B pathway in cuttlefish symbiotic accessory nidamental gland. Developmental & Comparative Immunology. Volume 53, Issue 1, November 2015, Pages 42–46


Cornet V, Henry J, Goux D, Duval E, Bernay B, Le Corguillé G, et al. (2015) How Egg Case Proteins Can Protect Cuttlefish Offspring? PLoS One 10(7): e0132836. doi:10.1371/journal.pone.0132836


Barbara Gasse; Xi Liu; Erwan Corre; Jean-Yves Sire. Amelotin gene structure and expression during enamel formation in the opossum Monodelphis domestica. PLoS One. 2015; 10(7): e0133314.


Zatylny-Gaudin, Celine; Cornet, Valérie; Leduc, Alexandre; Zanuttini, Bruno; Corre, Erwan; Lecorguillé, Gildas; Bernay, Benoît; Garderes, Johan; Kraut, Alexandra; Couté, Yohann; Henry, Joël. Neuropeptidome of the cephalopod Sepia officinalis: identification, tissue mapping and expression pattern of neurotransmitters and neurohormones during egg-laying. Journal of Proteome Research. Decembre 2015 DOI: 10.1021/acs.jproteome.5b00463


K. Wang, C. Del Castillo, E. Corre, E. Pales-Espinosa, and B. Allam, “Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology.,” BMC Genomics, vol. 17, no. 1, p. 146, 2016

Publications with the hosting laboratory

Toullec J-Y, Corre E, Bernay B, Thorne MAS, Cascella K, et al. (2013) Transcriptome and Peptidome Characterisation of the Main Neuropeptides and Peptidic Hormones of a Euphausiid: The Ice Krill, Euphausia crystallorophias. PLoS ONE 8(8): e71609. doi:10.1371/journal.pone.0071609


Janouškovec J, Liu SL, Martone PT, Carré W, Leblanc C, Collén J, Keeling PJ. 2013.Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.PLoS One. 2013;8(3):e59001. doi: 10.1371/journal.pone.0059001. Epub 2013 Mar 25.


Collén J., Porcel B., Carré W., Ball S., Chaparro C., Tonon T., Barbeyron T., Michel G., Noel B., Valentin K., Elias M., Artiguenave F., Arun A., Aury J.M., Barbosa-Neto J.F., Bothwell J.H., Bouget F.Y., Brillet L., Cabello-Hurtado F., Capella-Gutíerrez S., Charrier B., Cladière L., Cock J.M., Coelho S.M., Colleoni C., Czjzek M., Da Silva C., Delage L., Denoeud F., Deschamps P., Dittami S.M., Gabaldón T., Gachon C.M., Groisillier A., Hervé C., Jabbari K., Katinka M., Kloareg B., Kowalczyk N., Labadie K., Leblanc C., Lopez P.J., McLachlan D., Meslet-Cladiere L., Moustafa A., Nehr Z., Nyvall Collén P., Panaud O., Partensky F., Poulain J., Rensing S.A., Rousvoal S., Samson G., Symeonidi A., Weissenbach J., Zambounis A., Wincker P., Boyen C. 2013, Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5247-52. doi: 10.1073/pnas.1221259110.


Sophia Ahmed, J Mark Cock, Eugenie Pessia, Remy Luthringer, Alexandre Cormier, Marine Robuchon, Lieven Sterck, Akira F Peters, Simon M Dittami, Erwan Corre, Myriam Valero, Jean-Marc Aury, Denis Roze, Yves Van de Peer, John Bothwell, Gabriel A B Marais, Susana M Coelho (2014). A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. Current Biology : CB, 24(17), 1945–1957.


Godard, B. G., Coolen, M., Le Panse, S., Gombault, A., Ferreiro-Galve, S., Laguerre, L., Ronan Lagadec, Patrick Wincker, Julie Poulain, Corinne Da Silva, Shigehiro Kuraku, Wilfrid Carre, Agnes Boutet and Sylvie Mazan. (2014). Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates. Biology Open, 3(11), 1098–1107. doi:10.1242/bio.20148037


Kevin Cascella, Didier Jollivet, Claire Papot, Nelly Léger, Erwan Corre, Juliette Ravaux, Melody S. Clark and Jean-Yves Toullec.2014 Diversification, evolution and sub-functionalization of 70kDa heat-shock proteins in two sister species of Antarctic krill: Differences in thermal habitats, responses and implications under climate change.  PLoS One. 10(4):e0121642


Gregory K Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Corre and Laurence Garczarek. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics. 2015; 16(1): 281.  doi: 10.1186/s12859-015-0705-y


Simon M. Dittami, Laëtitia Duboscq-Bidot, Morgan Perennou, Angélique Gobet, Erwan Corre, Catherine Boyen, Thierry Tonon. Host-microbe interactions as a driver of brown algal acclimation to salinity gradients. The ISME Journal , (26 June 2015) | doi:10.1038/ismej.2015.104


Lipinska A, Cormier A, Luthringer R, Peters AF, Corre E, Gachon CMM, Cock JM, Coelho SM. 2014. Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga Ectocarpus. Mol Biol Evol. 2015 Jun;32(6):1581-97


Dominique Boeuf; Stephane Audic; Loraine Brillet-Gueguen; Christophe Caron; Christian Jeanthon. 2015. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution Database 2015; doi: 10.1093/database/bav080


James E. Tarver, Alexandre Cormier, Natalia Pinzón, Richard S. Taylor, Wilfrid Carré, Martina Strittmatter, Hervé Seitz, Susana M. Coelho and J. Mark Cock. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucl. Acids Res. (27 July 2015) 43 (13): 6384-6398.; doi: 10.1093/nar/gkv578


Sergio Balzano, Erwan Corre, Johan Decelle, Roberto Sierra, Patrick Wincker, Corinne Da Silva,  Julie Poulain, Jan Pawlowski, Fabrice Not. Transcriptome analyses to investigate symbiotic relationships between marine protists. Front Microbiol. 2015 Mar 17;6:98, section Microbial Physiology and Metabolism

cea
cnrs
inra
inria
inserm
logo_elixir
logo-investissements