The ABiMS (Analysis and Bioinformatics for Marine Science) platform at the Roscoff Biological Station is involved in a wide range of bioanalysis projects, primarily focusing on marine biodiversity, organismal genomics, and the functioning of microbial and planctonic communities. It supports research teams in analysing data generated by various omics approaches, from DNA and RNA sequencing to functional and environmental data.
Main types of bioanalysis projects
1. Genomics and comparative genomics
Genome assembly and annotation, functional annotation, genome comparison, gene family analysis, and studies of evolution and genetic diversity.
Examples: genomes of brown and red algae, cyanobacteria, archaea, and marine invertebrates; the ATLASea project.
2. Transcriptomics (RNA-seq)
Gene expression analysis, transcriptome assembly, identification of differentially expressed genes, and functional interpretation of biological responses.
Examples: environmental stress responses in microalgae and studies of reproduction and development in marine invertebrates.
3. Metagenomics and metabarcoding
Characterisation of taxonomic community composition, biodiversity assessment using environmental DNA (eDNA), community comparisons, and monitoring of changes over time and across locations.
Examples: plankton time series, coastal biodiversity, marine microbiomes, and Tara Oceans/Tara Pacific programmes.
4. Metatranscriptomics and viromics
Investigation of microbial community activity, environmental RNA analysis, characterisation of viral communities, and viral genome assembly.
Examples: marine viruses, plankton-associated microbial communities, and interactions between microorganisms.
5. Functional analyses and proteomics
Protein annotation, identification of domains and molecular functions, enzyme family analysis, and investigation of biological pathways.
Examples: algal enzymes, sulfotransferases and sulfatases, metabolic networks, and the functional potential of marine organisms.
6. Population genomics and phylogenetics
Analysis of genetic markers, SNPs and RAD-seq data, reconstruction of evolutionary relationships, and identification of signatures of selection or adaptation.
Examples: population differentiation, adaptive evolution, and comparisons of closely related marine species.
Beyond sequence analysis
ABiMS's involvement extends beyond bioinformatics analysis and the production of results. The platform also contributes to:
Developing reproducible pipelines, particularly for sequencing data processing and analysis on high-performance computing infrastructures.
Building scientific databases and portals, including search, visualisation, and genome exploration tools.
Managing and making data accessible, with a focus on documentation, interoperability, and FAIR principles (Findable, Accessible, Interoperable, Reusable).
Training and supporting researchers in bioinformatics methods and scientific computing environments.
