The Bioinformatics Service supports researchers of the Oceanological Observatory of Banyuls-sur-Mer  in the analysis, management and interpretation of biological data, with a particular focus on high-throughput sequencing.

It operates at the interface between biology and data science, working with all research units of the Observatory on projects ranging from evolutionary genomics to marine ecology and microbiology.

Missions

The service provides methodological and technical support throughout the lifecycle of research projects:

• analysis of genomic and transcriptomic data (NGS),

• development, adaptation and maintenance of analysis pipelines,

• design of new bioinformatics workflows tailored to specific scientific questions,

• guidance on experimental design and data production strategies,

• data management, storage and reproducibility,

• training and support for researchers, engineers and students.

Beyond data processing, the service contributes to defining appropriate analytical approaches, anticipating technical constraints and facilitating the use of shared computational resources.

Who is it for?

The service is open to all researchers, engineers, PhD students and trainees of the Observatory whether for:

• a specific analysis need,

• advice at the early stage of a project,

• support with data management,

• development of new bioinformatics approaches,

• training or skill development.

Contact

You can get in touch at any stage of your project — from initial idea to data analysis and interpretation.

Early discussions often help save time, secure methodological choices and optimize data production.

List of analyses that can be implemented quickly.

• Gene Expression
  • Differential expression – RNA-seq
• Epigenomics
  • DNA methylation (bisulfite sequencing)
  • ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing)
  • ChIP-seq (Chromatin Immunoprecipitation sequencing)
• De novo Assembly and annotation
  • Transcriptome assembly
  • Transcriptome clustering
  • Gene prediction
  • Gene prediction on a genome
• Gene Family Analysis
• Molecular Phylogeny

The catalogue of common analyses will be updated according to your needs and the evolution of the service.
For analyses not listed here, feel free to contact us: bsbii « @ » obs-banyuls.fr

Bioinformatics analysis catalogue

The service provides a set of analyses that can be implemented rapidly using established, documented and reproducible pipelines. This catalogue evolves according to research needs, ongoing projects and methodological developments.

Transcriptomics

• Gene expression analysis

• Differential expression analysis (RNA-seq)

• Transcriptome assembly and analysis

• Transcript clustering and functional annotation

Genomics

• De novo genome assembly

• Hybrid assembly (short and long reads)

• Structural and functional genome annotation

• Gene family analysis

• Comparative genomics and evolutionary analyses

Epigenomics and gene regulation

• DNA methylation analysis (bisulfite sequencing)

• ATAC-seq (chromatin accessibility)

• ChIP-seq (DNA–protein interactions)

• Gene regulatory network (GRN) inference

Metagenomics and microbial ecology

• Metagenomic and metatranscriptomic data analysis

• Taxonomic assignment (alignment-based or k-mer approaches)

• Community structure and diversity analyses

Phylogeny and evolution

• Molecular phylogenetics

• Multi-species comparative analyses

• Gene and genome evolution studies

Data management and reproducibility

• Development and adaptation of analysis pipelines

• Workflow documentation, traceability and reproducibility

• Research data organisation, storage and security

• Preparation and submission of datasets to public repositories (FAIR principles)

This catalogue reflects analyses routinely performed within research projects at the Observatory and can be adapted to specific scientific questions, data types and project needs.

Researchers are encouraged to contact the service to discuss a project, dataset or methodological approach.

Bioinformatics training and support

BSBII offers training sessions designed for researchers, engineers and graduate students who wish to develop practical skills for handling biological data and computational environments.

These trainings focus on real research use cases and aim to make participants operational quickly, whether they are starting in bioinformatics or looking to strengthen specific skills.

Main training topics

• Linux for biologists (command line, file systems, remote environments)

• Introduction to Python for data analysis

• Use of shared computing infrastructures (HPC, clusters, job schedulers)

• Good practices for data organisation, reproducibility and documentation

• Introduction to NGS data analysis workflows

Sessions combine short theoretical inputs with hands-on exercises based on biological datasets. They can be delivered:

• as scheduled group sessions,

• within institutional training programmes,

• or tailored to the needs of a research team.

If you are interested in a training session for your team or unit, feel free to contact the service.