About us
SeBiMER - Marine Bioinformatics Platform
SeBiMER is the marine bioinformatics core facilities operated by Ifremer, the French National Institute for Ocean Science.
A team of engineers is in charge of providing a large community of marine biologists with all the requirements (knowledge, software and data) to handle small- and large-scale bioinformatics projects, mostly in three main fields: metabarcoding and metagenomics (eDNA), (meta-)transcriptomics and genomes assembly & annotation.
 |
SeBiMER is member of Biogenouest, the network of technological core facilities of the Western France in life sciences and the environment. |
As an open core facilities, SeBiMER can provide technical and scientific support to bioinformatics projects out of Ifremer.
SeBiMER operates all bioinformatics activities on DATARMOR supercomputer hosted at Ifremer.
Our missions
The platform’s missions are organized in four poles:
Bioanalysis
Involvement in research projects to provide technical, scientific and data analysis expertises.
System and software engineering
Design of new tools and data analysis workflows optimized for high performance computing.
Platform management
Bioinformatics data management and software installation & configuration on DATARMOR supercomputer.
Trainings
Bioinformatics training covering the above fields.
Project support
The SeBiMER team is involved in many projects
Genome assembly
Example of recent projects
Metabarcoding
Example with recent projects
Metagenomics
Example with recent projects.
Transcriptomics
Example with recent projects
Data management
FAIR bioinformatics data management
Workflow engineering
Pipelines created by SeBiMER
Software engineering
Softwares contributed by SeBiMER
Galaxy
The Galaxy platform at Ifremer
Training
SeBiMER training catalog
Publications
SeBiMER publications and contributions
SeBiMER Team
Patrick Durand
Director, Bioinformatics PhDDevelopper, data management, Java, container
Laura Leroi
Bioinformatics engineerGalaxy Admin, data management, git, IT automation system, python
Cyril Noel
Bioinformatics PhDMetabarcoding, metagenomics, statistics, transcriptomics, workflow, R
Alexandre Cormier
Bioinformatics PhDGenome assembly and annotation, phylogenomics, transcriptomics, data processing, python, git
Pauline Auffret
Bioinformatics engineerDevelopper, workflow, data management, transcriptomics, Nextflow
David Goudenège
Bioinformatics PhDGenome annotation, comparative genomics, phylogenomics, variant calling, developper, python, bash
Marie Jossé
Bioinformatics engineerGalaxy, developper, cloud, python, git
Frequently Asked Questions
-
Who do we collaborate with?
Research teams of French research institutes such as Ifremer, INRAe, CNRS, Université de Montpellier, Université de Bretagne Occidentale, Université de Pau et des Pays de l'Adour.
Among foreign parterns, we collaborate with researchers from the University of Würzburg (Germany), University of Laval (Canada), University of Minnesota (USA), Texas State University (USA).
-
How to interact with us?
Ifremer and affiliate labs can contact us directly using our helpdesk email address.
Others, please use the form below to contact the SeBiMER team.