Analysis and Bioinformatics for Marine Science

Description

Type of entity	Platform
Main activity	ABiMS offers analysis and developments to research teams within the framework of scientific collaborations formalised as projects. Its service offer is divided in five activities:access to hardware and software environments (HPC cluster, Galaxy, Cloud) e-infrastructure: High Performance Computer, Galaxy, JBrowse/Apollo, RStudio, databanks, storage and bioinformatics software Bioinformatics analysis: '-omics' data analysis (RNAseq, assembly, metagenomics, metabarcoding, etc.) Software engineering: web appliance, software, database creation Training: RNASeq, phylogeny, Linux, R, Python Support: support request for the use of platform resources (software, data, etc.) ABiMS belongs to national infrastructures: the French Institute of Bioinformatics (IFB) and the EMBRC-France resource center.
Keywords	Bioinformatics, HPC, Storage, Analysis services, Softare engineering, Database management
Labels	Biogenouest Recognised French National Research Infrastructure (IR) EMBRC-France EMBRC-ERIC Elixir ODATIS French Institute of Bioinformatics
Website Plug in labs Ouest
Related entities
Databases
High Performance Computer constituted of 1800 CPU
Software

Services

Bioinformatics analysis Recherche

E-infrastructure Recherche

Training

Software engineering in Life Sciences and Oceanography Recherche

Owned/operated by

Website Roscoff Marine Station

Website Sorbonne University

Location and contact

	Send an e-mail
Adress	Place Georges Teissier
Address line 2	Station Biologique de Roscoff - CS 90075
Zip code/Postcode	29688
Town/city	ROSCOFF

Services

Concerned publics	Companies Research partners Other researchers
Terms of access	Research collaboration access Supervised access
Access url	http://abims.sb-roscoff.fr/account
Description	Access to computing infrastructure providing computing server ranging from 32 GB to 2 TB. Storage up to 1.7 PB

Bioinformatics analysis Recherche

Concerned publics	Research partners
Terms of access	Research collaboration access
Access url	http://abims.sb-roscoff.fr/projects/request
Description	Analysis of data from several ?omics' projects covering a large diversity of marine living organisms (from bacteria to archaea, from fungi to seaweeds, from protists to larger metazoan)

E-infrastructure Recherche

Concerned publics	Research partners
Terms of access	Research collaboration access
Access url	http://abims.sb-roscoff.fr/projects/request
Description	Access to databases are provided to different applications (CLI software, Galaxy workflows) in several indexing formats (Blast, Bowtie, BWA, ?). Most of them are automatically downloaded and formatted using BioMAJ

Training

Concerned publics	Research partners
Terms of access	Research collaboration access
Access url	http://abims.sb-roscoff.fr/training
Movable ?	yes no

Software engineering in Life Sciences and Oceanography Recherche

Concerned publics	Research partners
Terms of access	Research collaboration access
Access url	http://abims.sb-roscoff.fr/projects/request
Movable ?	yes no
Description	Software engineering as carried out by ABiMS aims to provide research teams and user communities with databases or tools that best suit their needs

Description

Certification, standardization, calibration
Category	Software Digital Modelling and in situ data providers Scientific computing
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Scientific disciplines	Bioinformatics Metrology Microbiology Marine Ecology Genomics / Genetics Marine biology
Strategic areas of action	Marine energy and mining resources Environmental and coastal planning and development
Examples of work	Elixir (UE). EMODNet Biology Associated Data Partner. Idealg, Oceanomics. ANR projects: Cinnamon, Impekab, Hapar, ?
URL works	http://abims.sb-roscoff.fr/projects

Owned/operated by

Website Roscoff Marine Station
The Roscoff Marine Station is a research and teaching centre for marine biology and ecology. It depends on the CNRS and Sorbonne University.

Website Sorbonne University
Sorbonne University is a multidisciplinary, research-intensive and world-class academic institution. Firmly rooted in the heart of Paris, it is committed to the success of its students and devoted to meeting the scientific challenges of the 21st century.