BiRD

Adress
IRS UN, 8 Quai Moncousu 44000 Nantes
Structure(s)
INSERM, CNRS
Unit:
UMR INSERM 1087/CNRS 6291, UMS INSERM 016/CNRS 3556
[field_pole_regional_de_rattachem]
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • Label IBiSA
Infrastructure
Propriétaire
Effective storage
700.00 To
Cluster: cores number
992 cores
Data collections number
8
CPU/hours a year
3 559 638 H / an
Bioinformatic tools number
23
Users number (last year)
117
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:


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 Pipeline

Description

Analysis pipeline using Snakemake for transcriptome profiling by 3' RNA sequencing.

Access conditions

This pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline

 

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

DEPIB

Description

Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.

Access conditions

This pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipe...

 

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

microSysMics

Description

This 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 conditions

This 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 language

Description

OBJECTIVES :

* Acquire basic knowledge on the R language
* Experience the main features of R
* Be autonomous in handling data
* Perform simple statistical analysis and build charts
* Learn how to create functions

Access conditions

This 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 analysis

Description
Objectives :
  •     Understand the main steps in analyzing RNAseq data for a differential gene expression study
  •     How to perform a command line analysis with Snakemake

Alternating between theoretical and practical parts.

Prerequisite: knowledge of command line usage or having followed the "Introduction to the command line" training course.

Access conditions

This 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 initiation

Description

Objectives :

  •     Knowing the principles and advantages of the Linux system
  •     Knowing how to use the main bash commands
  •     Knowing how to launch programs with arguments
  •     Acquiring autonomy to perform bioinformatics analysis on the command line.
Access conditions

This 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
"Fine-scale human genetic structure in Western France", European Journal of Human Genetics, vol. 23, no. 6, pp. 831–836, 2015.
"From scientific workflow patterns to 5-star linked open data", {TaPP} 2016: 8th {USENIX} {Workshop} on the {Theory} and {Practice} of {Provenance}, Washington D.C., United States, 2016.
"Targeted resequencing identifies TRPM4 as a major gene predisposing to progressive familial heart block type I", International Journal of Cardiology, vol. 207, pp. 349–358, mar, 2016.
"SHARP: Harmonizing and Bridging Cross-Workflow Provenance", The {Semantic} {Web}: {ESWC} 2017 {Satellite} {Events}, vol. 10577, Cham, Springer International Publishing, pp. 219–234, 2017.
"SHARP: Harmonizing Galaxy and Taverna workflow provenance", {SeWeBMeDA} 2017 : {Semantic} {Web} solutions for large-scale {BioMedical} {Data} {Analtics} - 14th {ESWC} 2017, Portoroz, Slovenia, 2017.
External publications
"Correction: The genetic history of France", European Journal of Human Genetics, pp. 1–1, mar, 2020.
"Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration", International Journal of Molecular Sciences, vol. 21, no. 4, pp. 1368, jan, 2020.
"The paracaspase MALT1 cleaves the LUBAC subunit HOIL1 during antigen receptor signaling", Journal of Cell Science, vol. 129, no. 9, pp. 1775–1780, may, 2016.
"De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability", The American Journal of Human Genetics, vol. 101, no. 5, pp. 768–788, 2017.
"Extensive recent secondary contacts between four European white oak species", New Phytologist, vol. 214, no. 2, pp. 865–878, apr, 2017.
"Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities", Future Generation Computer Systems, vol. 75, pp. 284–298, oct, 2017.
"Efficient Mitochondrial Glutamine Targeting Prevails Over Glioblastoma Metabolic Plasticity", Clinical Cancer Research, vol. 23, no. 20, pp. 6292–6304, 2017.
"Parallel derivation of isogenic human primed and naive induced pluripotent stem cells", Nature Communications, vol. 9, no. 1, pp. 360, 2018.
 
Publications with the hosting laboratory
 
Users distribution
International
3 %
National
17 %
Regional
27 %
Local
53%
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
(3)

Développement de pipelines d'analyse :

  • 3'seq RNA profiling
  • SingleCell transcriptomics
  • Microbiote analysis
Collaborations
National projets
Not documented
International and European projects
(1)

ELIXIR Interoperabillity Platform

The goal of the Interoperability Platform is to help people and machines to discover, access, integrate and analyse biological data. It encourages the life science community to adopt standardised file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals.
Projects with industry
Not documented
Collaboration projects not founded through an external organism
(5)

INEX-MED

Alban Gaignard leads INEX-MED project : INtegration and EXploration of heterogeneous bio-MEDical data. The objective of this pilot project supported by the IFB is to develop a sustainable infrastructure for integration, exploitation and modelling (semantic/statistical) on heterogeneous data sources and multi-site computing infrastructures in the biomedical area.
 

Mibiogate

Philippe Bordron and Erwan Delage are involved in the Mibiogate project.
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

CEPH Recherche : Pilot project for the secure storage of massive research data using CEPH technology on a principle of sharing equipment and staff of partner members : CCIPL, BiRD, LS2N, CEISAM, DSIN.
 

IFB Biosphere

IFB Biosphère : French Institute of Bioinformatics (IFB) provides life scientists with a federation of clouds, Biosphere, and bioinformatics cloud services to analyze life science data. Biosphere is used for scientific production in the life sciences, developments, and to support events like cloud and scientific training sessions, hackathons or workshops.
 
 
Provision of services not founded through an external organism
(45)
En 2019, 45 projets académiques en prestation de bio-analyse ont été menés dont : - 2 projets de génotypage - 1 projets de RNAseq - 42 projets de 3'Seq-RNA Profiling
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'.

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