Projects

ABiMS is involved in several scientifics projects :

With the research teams from the "Station Biologique de Roscoff",
As well as partnerships with external teams (Paris, Caen, Nantes, Brest, Toulouse, Clermont-Ferrand, etc.),
And also several institutes (Universities, CEA, CNRS, UPMC, IFREMER, INRA, INSERM, etc.).

National projects

The ABIMS platform is involved in many national projects, including several from the "ANR Investissements d'Avenir": PIA3

MuDi4LS : Mututalised Digital Spaces for FAIR Life Sicences
AO-EMBRC : Augmented-Observatories of EMBRC
The EMERGEN consortium : conducting genomic surveillance of SARS-CoV-2 variants in France.
ABROMICS : a digital platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data
PPR : FUTURE-OBS : Augmented Observatory for Coastal Socio-ecosystems
PEPR : ATLASEA : Atlas des génomes marins : des données massives à l’innovation

former projects :

EMBRC-France (2011/2020): coordination of marine model data integration and link with other IA projects like TefoR
IDEALG (2011/2021): e-infrastructures development and implication in bio-analyses tasks
OCEANOMICS (2012/2021): data integration
"Institut Français de Bio-informatique" (2012/2020): infrastructure providers, participation and coordination of the NNCR, link with Marine community and platforms devoted to vegetal (URGI, CIRAD, etc.); workflow devlopments (1rst part of teh project)

ANR BONUS / A.C. Baudoux (2023/2026)
ANR SEABIOZ / P. Potin (2021/2026)
ANR CoPilot / G. Mauduire (2020/2022)
ANR CINNAMON / L. Garckzarek (2017-2022)
ANR IMPEKAB /F. Not (2015/2021)
ANR HAPAR / L. Guillou (01/10/2014 - 30/09/2018)
ANR SAMOSA / F. Partensky (2013/2017)
ANR VIBRIOGEN / F. Le Roux (2011/2014)
ANR PELICAN / F. Partensky (2009/2013)
ANR Jeunes Chercheurs BROWNSUGAR / C. Hervé (2021-2024)
ANR Jeunes Chercheurs ALGAVOR / F.Thomas (2018-2022)
ANR Jeunes Chercheurs CALYpSO / A.C. Baudoux (2015-2019)
ANR Jeunes Chercheurs ISOBAR / T. Broquet (2013/2017)
ANR Jeunes Chercheurs SEXSEAWEED / S. Coehlo (2012/2015)

BenthOBS SNO: Benthic Macrofauna Communities National Observation Network. PHYTOBS is a labeled National Observation Network aiming to collect long-term environmental datasets about benthic macrofauna gathered form over 20 stations, operated by the CNRS, Universities and IFREMER. ABiMS is in charge of the data ingestion and access layers allowing the Web portal do offer data browsing/searching and download features.
PHYTOBS SNO : Phytoplankton Observation National Observation Network. PHYTOBS is a labeled National Observation Network aiming to collect long-term environmental datasets about phytoplankton biodiversity gathered form over 20 stations, operated by the CNRS, Universities and IFREMER. ABiMS is in charge of the data ingestion and access layers allowing the Web portal do offer data browsing/searching and download features.
The PELAGOS V2 project stems from a collaborative work from "Réseau des Stations et Observatoires Marins" (RESOMAR). It offers database management tools for collaborative work for the help in collaborative work, for biological data from pelagic compartment (microorganism and macroorganism). Two videos are published online in order to present the display interface and a dedicated extension for data analysis under Galaxy.
High-Frequency database (Pascal Morin).

Dinoflagellate parasite Amoebophrya
Brown seaweeds Ectocarpus siliculosus and France Genomic Phaeoexplorer project
Red seaweeds genome Chondus crispus
Little shark genome Scyliorhinus canicula (Sylvie Mazan team)

EOSC Life (2019-2023) project, part of the WP2 (Workflow). We contributed to the demonstrator 4 use case developed by the CCMAR that was addressing the transfer of genome annotations between closely related marine species – as a test case, pelagic fishes - using genome synteny relationships. In this context, we have integrated necessary tools into Galaxy and the Toolshed (LAST tools for genome comparison and alignment, gffalign to for gene extraction and annotations transfer using genome synteny), and we have developped a Galaxy Docker image containing the workflow tools, available on quay.io. We have also developped Ansible recipes to allow the deployment of a Virtual Machine in a an Openstack cloud via the Terraform software, the installation of the GGA environment and its dependencies, as well as loading data into the Galaxy library. The Galaxy Genome Annotation (GGA) project consists of several projects and tool suites that are working closely together to deliver a comprehensive, scalable and easy to use Genome Annotation experience.
ELIXIR Excellerate H2020 (2015/2019): participant to of the WP6 Marine metagenomics, co leader of the Galaxy community
EMBRIC H2020 (2015/2019): European Marine Biological Research Infrastructure Cluster
Information system and shared database from ASSEMBLE European project (2009-2012)
Infrastructure set up for genomic data management from ESFRI EMBRC project