

BiRD
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
Structure(s)
Unit:
Website
bird.univ-nantesScientific leader(s)
Technical leader(s)
Certificat(s)
- Label IBiSA
Infrastructure
Effective storage
Cluster: cores number
Data collections number
CPU/hours a year
Bioinformatic tools number
Users number (last year)
Servers description
BiRD provides the community with a high-performance, equipped and secure IT infrastructure for computing and hosting your scientific data. The software environment is constantly evolving with the ongoing addition of new tools according to your requests.
The platform is equipped with:
- a computing cluster open to the scientific community
- 14 nodes for a total of 832 threads and 3.8 TB RAM
- an associated 400TB scratch storage and 250TB of securized storage
- a CLOUD platform under OpenStack
- 160 threads
- 50 TB of storage
Access conditions
Ask for an account : pf-bird@univ-nantes.fr
The charter could be found here : http://www.pf-bird.univ-nantes.fr
![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
3SRP PipelineDescriptionAnalysis pipeline using Snakemake for transcriptome profiling by 3' RNA sequencing. Access conditionsThis pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline
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![]() Annual visits: Not documented
Unique visits: Not documented
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DEPIBDescriptionAnalysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes. Access conditionsThis pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipe...
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![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
microSysMicsDescriptionThis workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis. Access conditionsThis pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics |
Domains of activity
- Biomedical
- Biology
- Computer Science
Description of expertise domains
BiRD advises, proposes and develops bioinformatics services: analysis of high throughput sequencing data for variant detection, transcriptome study and now microbiote analysis. To this end, BiRD works jointly with the Genomic core facility, which handles library preparation and sequencing projects.
For all these applications, BiRD has expertise in large-scale data analysis and has developed dedicated bioinformatics analysis pipelines to standardize analysis from raw data to biological interpretation.
These services are supported by a dedicated computing and storage infrastructure, remotely accessible through several services and open to the scientific community regardless of its institution.
Member of the Federative Research Structure François Bonamy, BiRD core facility leans on the research teams in human genetics and genomics at the institut du thorax. One of the scientific aims of these teams is to elucidate the molecular mechanisms of cardiovascular pathologies (sudden death, arrhythmias, valvulopathies, cerebral aneurysms, etc.). The analysis strategies used are based on high-throughput genomic screening technologies coupled with the development of new dedicated bioinformatics tools, with the aim of identifying new risk markers in these pathologies.
The core facility works also with the Combi team of the LS2N (Laboratoire des Sciences Numériques Nantes), whose main research themes focus on comparative genomics and systems biology. The main research axes developed in this team are :
- From genome to graph comparison
- From biological process modeling to community modeling
- Linking modeling scales to extract biomarkers
- Bioinformatics developments
Keywords:
- NGS data analysis
- Transcriptomics (RNA-seq)
- Differential gene expression analysis
- Variant calling
- Panels (amplicons, captures)
- Exomes
- Whole genomes
- Metagenomics, metatranscriptomics
- Machine learning
- Knowledge extraction
- Integration of heterogeneous data
- Knowledge representation
- Ontologies
- Semantic Web
- System biology
- Complex biological systems functions
- Metabolic engineering
- Multi-layer analysis and modelling
- Metabolic network modelling
- Regulatory network modelling
- System modelling
- Dynamic systems
- Information and communication technology developments
- Tools
- Tool integration
- Interoperability
- Workflows developments
- Data
- Data integration
- Data management and transfer
- Computing environments
- Cluster
- Cloud
- Ecology
- Biodiversity
- Microbial ecology
- Modelling in ecology
Formation professionnelle
![]() Trainees: 20 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Initiation to R languageDescriptionOBJECTIVES : * Acquire basic knowledge on the R language Access conditionsThis training is open to all (public and private) with no institution restrictions and is accessible through the University of Nantes continuing education programme. |
![]() Trainees: 10 trainees / year
Training time: 3 day(s) / year
No upcoming session scheduled
RNASeq data analysisDescription
Objectives :
Alternating between theoretical and practical parts. Prerequisite: knowledge of command line usage or having followed the "Introduction to the command line" training course. Access conditionsThis training is open to all (public and private) with no institution restrictions and is accessible through the University of Nantes continuing education programme. |
![]() Trainees: Not documented
Training time: Not documented
No upcoming session scheduled
Command line initiationDescriptionObjectives :
Access conditionsThis training is open to all (public and private) with no institution restrictions and is accessible through the University of Nantes continuing education programme. |
Internal publications
External publications
Publications with the hosting laboratory
Users distribution
Explanation about this distribution:
BiRD is part of Biogenouest, the network of core facilities working in life science across western France (Brittany and Pays de Loire). Therefore, it maintains a privileged relationship with the academic laboratories residing in western france, but remains open to any other public institution or private organisation.
Platform's own projects
Développement de pipelines d'analyse :
- 3'seq RNA profiling
- SingleCell transcriptomics
- Microbiote analysis
Collaborations
National projets
International and European projects
ELIXIR Interoperabillity Platform
Projects with industry
Collaboration projects not founded through an external organism
INEX-MED
Mibiogate
Philippe works more specifically in the analysis and interpretation of transcriptomic data from host organs in the context of stress studies on barriers.
Erwan works on the implementation of tools for the analysis and integration of metagenomic, biological and clinical data for the study of chronic pathologies and more particularly on the development of a complete metagenomic analysis pipeline (from raw sequences to the construction of gene catalogues, the reconstruction of genomes and the generation of tables of abundance at the taxonomic and functional level).
Mibiogate is a project to study biological barriers and their microbiota in the development of chronic diseases, supported by the Pays de la Loire Region. The consortium created aims to structure a research network specialized in the study of the dysfunctions of the biological barriers of the different organs in chronic pathologies of interest.
CEPH Recherche
IFB Biosphere
Provision of services not founded through an external organism
Animations (Workshops, Work-groups, seminars, conferences ... )
- The 'Bioinformatics Breakfasts' : informal meetings that bring together regional actors in bioinformatics, with the aim to share experiences in selected topics in a friendly atmosphere.
- The 'Scientific Day' of Biogenouest Bioinformatics core facilities is organised once a year. The last edition took place in December 2015 under the theme 'New sequencing technologies and applications in Health and Environment'.