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
E-infrastructure
Training
Software engineering in Life Sciences and Oceanography
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
Description Access to computing infrastructure providing computing server ranging from 32 GB to 2 TB. Storage up to 1.7 PB
Concerned publics Companies
Research partners
Other researchers
Terms of access Research collaboration access
Supervised access
Access url http://abims.sb-roscoff.fr/account
Bioinformatics analysis
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)
Concerned publics Research partners
Terms of access Research collaboration access
Access url http://abims.sb-roscoff.fr/projects/request
E-infrastructure
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
Concerned publics Research partners
Terms of access Research collaboration access
Access url http://abims.sb-roscoff.fr/projects/request
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
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
Concerned publics Research partners
Terms of access Research collaboration access
Access url http://abims.sb-roscoff.fr/projects/request
Movable ? yes no
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.
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