BiRD

Adress
IRS UN, 8 Quai Moncousu 44000 Nantes
Structure(s)
INSERM
Unit:
UMR INSERM 1087
Regional Center
IFB West
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • ISO 9001
Infrastructure
Propriétaire
Effective storage
150.00 To
Cluster: cores number
320 cores
Data collections number
8
CPU/hours a year
79 863 H / an
Bioinformatic tools number
23
Users number (last year)
92
Servers description
  • HPC cluster dedicated to NGS data analysis and pipeline developpement:
    • 8 nodes = 512 cores and 2.1 To RAM.
    • 138 To of effective storage (RAID 5)
    • HPC Storage : Parallel file system (BeeGFS)
  • HPC cluster open to the scientific community (hosted in the datacenter of the university of Nantes) :
    • 5 nodes = 320 cores and 1.3 To RAM
    • 150 To of effective storage (RAID 5)
  • 2  Galaxy servers (production & development)
  • 3 servers (web, files & development)

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

Galaxy-LD

Description

Galaxy-LD is a tool dedicated to the generation of provenance graphs (RDF, PROV-O ontology) based on Galaxy user histories. The tool is currently available through a command line interface. A web-based user interface is under active development.

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

SHARP-prov-toolbox

Description

SHARP-prov-toolbox is a tool aimed at harmonizing heterogeneous provenance graphs based on reasoning (PROV inferences). PROV Constraints inferences rules have been implemented through the JENA forward chaining inference engine.

Access conditions
Annual visits:
Not documented
Unique visits:
26 an
Quotes:
Not documented
Downloads:
Not documented

Galaxy@BiRD

Description

Le portail Galaxy de BiRD propose des outils pour l'analyse de données de :

  • séquençage NGS : analyse de variants et transcriptomique
  • puces à ADN
  • puces à protéines

 

 

Access conditions

L'accès à Galaxy nécessite la création d'un compte sur le cluster : http://www.pf-bird.univ-nantes.fr/07074276/0/fiche___pagelibre/&RH=14425...

 

Domains of activity
  • Biomedical
  • Biology
  • Computer Science
Description of expertise domains

BiRD has initially developed its expertise in the field of transcriptome data analysis from microarray. Since 2012, BiRD has completed its know-how with the development and/or implementation of methods and tools for NGS data analysis.

A wide range of applications are supported, in particular in the fields of genetics (whole genome, full exome, targeted sequencing) and gene expression analysis (RNASeq).

The development of NGS pipelines is mainly based on the "make" tool, which is used in a distributed job management environment, allowing parallel computing tasks.

by these developments, BiRD has become - in connection with the Genomics Platform of Nantes (Biogenouest Genomics) - a service provider for the 'Fondation Maladies Rares' in the context of its calls for whole exome sequencing project. Seven projects have been supported since mid-2013, corresponding to the analysis of 86 full exome sequences.
 
On one side, BiRD is member of l'institut du thorax (Inserm UMR 1087 / CNRS UMR 6291) and develops its research in close connection with two teams working on cardiovascular genetics. On the other side, the core facility is part of the
LINA (Laboratoire Informatique Nantes Atlantique) and collaborates with the team Combi, whose main objective is the development of mathematical methods in comparative genomics and systems biology.

Together, the geneticists of l'institut du thorax and the computer scientists of the LINA define the strategic orientations of BiRd, and manage its human resources and IT investments.

In addition to its core activities, BiRD works regularly with particular users who wish to develop dedicated NGS-based methods. As an example, the platform has contributed to the development of novel tools for characterizing viral integration patterns in muscle cell genomes in the context of gene therapy (see Cogné et al, Nat Med 2014; 20: 577-8).

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
  • Biostatistics
  • Descriptive statistics
  • Statistical tests
  • Regression
  • Multivariate analysis
  • Dimension reduction
  • Inferences and biological network analysis
  • Genetic statistics
  • 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
  • Genomics: Chips
  • DNA chips
  • Genotyping
  • CGH
  • RNA chips
  • Expression

Formation professionnelle

Trainees:
20 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

initiation to the 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 available through continuing education of INSERM

Trainees:
10 trainees / year
Training time:
3 day(s) / year
No upcoming session scheduled

Gene expression data analysis with Galaxy (microarray)

Description
Objectives :

* Assimilate the concepts and methods related to gene expression analysis from microarray data (Affymetrix/Agilent)
* Learn how to analyze transcriptome data (microarray) under the Galaxy environment
* Learn more about biological data interpretation

Theory: 30% / Practice : 70%
One workstation per student.
Participants who wish may, on the last day, analyze their own dataset.

Access conditions

This training is available through continuing education of INSERM

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

Développement de pipelines d'analyse de données génomiques.

Collaborations
National projets
- Projet INCa : «Structuration du séquençage de nouvelle génération à visée diagnostique en cancérologie»

- ANR CavsGen (Blanc - SVSE 6) : Variation génétique, transcriptome et épigénome du rétrécissement aortique calcifié

International and European projects
Not documented
Projects with industry
Not documented
Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
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'.

Internal publications

Alban Gaignard, Hala Skaf-Molli , Audrey Bihouée
From scientific workflow patterns to 5-star linked open data
TaPP'16 Proceedings of the 8th USENIX Conference on Theory and Practice of Provenance

External publications
Picarda E, Bézie S, Boucault L, Autrusseau E, Kilens S, Meistermann D, Martinet B, Daguin V, Donnart A, Charpentier E, David L, Anegon I, Guillonneau C.
Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells
JCI Insight. 2017 Feb 9;2(3):e90088. doi: 10.1172/jci.insight.90088.
 

Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil , Hervé Ménager, Christophe Pradal, Christophe Blanchet.
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
Future Generation Computer Systems · January 2017


Isidor B, Küry S, Rosenfeld JA, Besnard T, Schmitt S, Joss S, Davies SJ, Lebel RR, Henderson A, Schaaf CP, Streff HE, Yang Y, Jain V, Chida N, Latypova X, Caignec CL, Cogné B, Mercier S, Vincent M, Colin E, Bonneau D, Denommé AS, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Piton A, Dina C, Donnart A, Lindenbaum P, Charpentier E, Redon R, Iemura K, Ikeda M, Tanaka K, Bézieau S.
De Novo Truncating Mutations in the kinetochore-microtubules attachment gene CHAMP1 Cause Syndromic Intellectual Disability
Hum Mutat. 2016 Jan 11. doi: 10.1002/humu.22952

Lecomte E, Tournaire B, Cogné B, Dupont JB, Lindenbaum P, Martin-Fontaine M, Broucque F, Robin C, Hebben M, Merten OW, Blouin V, François A, Redon R, Moullier P, Léger A.
Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing.
Mol Ther Nucleic Acids. 2015 Oct 27


Shy D, Gillet L, Ogrodnik J, Albesa M, Verkerk AO, Wolswinkel R, Rougier JS, Barc J, Essers MC, Syam N, Marsman RF, van Mil AM, Rotman S, Redon R, Bezzina CR, Remme CA, Abriel H.
PDZ domain-binding motif regulates cardiomyocyte compartment-specific NaV1.5 channel expression and function.
Circulation. 2014 Jul 8;130(2):147-60


Cogné B, Snyder R, Lindenbaum P, Dupont JB, Redon R, Moullier P, Leger A.
Artefactual integration sites of AAV vectors generated by NGS library preparation.
Nat Med. 2014 Jun;20(6):577-8


Mercier S, Küry S, Shaboodien G, Houniet DT, Khumalo NP, Bou-Hanna C, Bodak N, Cormier-Daire V, David A, Faivre L, Figarella-Branger D, Gherardi RK, Glen E, Hamel A, Laboisse C, Le Caignec C, Lindenbaum P, Magot A, Munnich A, Mussini JM, Pillay K, Rahman T, Redon R, Salort-Campana E, Santibanez-Koref M, Thauvin C, Barbarot S, Keavney B, Bézieau S, Mayosi BM.
Mutations in FAM111B Cause Hereditary Fibrosing Poikiloderma with Tendon Contracture, Myopathy, and Pulmonary Fibrosis.
Am J Hum Genet. 2013 Dec 5;93(6):1100-7. doi:10.1016/j.ajhg.2013.10.013. Epub 2013 Nov 21.


Colman H, Le Berre-Scoul C, Hernandez C, Pierredon S, Bihouée A, Houlgatte R, Vagner S, Rosenberg AR, Féray C.
Genome-wide analysis of host mRNA translation during hepatitis C virus infection.
J Virol. 2013 Apr 3.
Publications with the hosting laboratory
Sanchez-Castro M, Eldjouzi H, Charpentier E, Busson PF, Hauet Q, Lindenbaum P, Delasalle-Guyomarch B, Baudry A, Pichon O, Pascal C, Lefort B, Bajolle F, Pezard P, Schott JJ, Dina C, Redon R, Gournay V, Bonnet D, Le Caignec C.
Search for Rare Copy-Number Variants in Congenital Heart Defects Identifies Novel Candidate Genes and a Potential Role for FOXC1 in Patients With Coarctation of the Aorta.
Circ Cardiovasc Genet. 2016 Feb;9(1):86-94. doi: 10.1161/CIRCGENETICS.115.001213. Epub 2015 Dec 7.

Rimbert A, Pichelin M, Lecointe S, Marrec M, Le Scouarnec S, Barrak E, Croyal M, Krempf M, Le Marec H, Redon R, Schott JJ, Magré J, Cariou B.
Identification of novel APOB mutations by targeted next-generation sequencing for the molecular diagnosis of familial hypobetalipoproteinemia.
Atherosclerosis, 2016


Daumy X, Amarouch MY, Lindenbaum P, Bonnaud S, Charpentier E, Bianchi B, Nafzger S, Baron E, Fouchard S, Thollet A, Kyndt F, Barc J, Le Scouarnec S, Makita N, Le Marec H, Dina C, Gourraud JB, Probst V, Abriel H, Redon R, Schott JJ
Targeted resequencing identifies TRPM4 as a major gene predisposing to progressive familial heart block type I.
International Journal of Cardiology (2016), doi:10.1016/j.ijcard.2016.01.052


Le Scouarnec S, Karakachoff M, Gourraud JB, Lindenbaum P, Bonnaud S, Portero V, Duboscq-Bidot L, Daumy X, Simonet F, Teusan R, Baron E, Violleau J, Persyn E, Bellanger L, Barc J, Chatel S, Martins R, Mabo P, Sacher F, Haïssaguerre M, Kyndt F, Schmitt S, Bézieau S, Le Marec H, Dina C, Schott JJ, Probst V, Redon R.
Testing the burden of rare variation in arrhythmia-susceptibility genes provides new insights into molecular diagnosis for Brugada syndrome.
Hum Mol Genet. 2015 May 15;24(10):2757-63. doi: 10.1093/hmg/ddv036. Epub 2015 Feb 3.


Karakachoff M, Duforet-Frebourg N, Simonet F, Le Scouarnec S, Pellen N, Lecointe S, Charpentier E, Gros F, Cauchi S, Froguel P, Copin N; D.E.S.I.R. Study Group, Le Tourneau T, Probst V, Le Marec H, Molinaro S, Balkau B, Redon R, Schott JJ, Blum MG, Dina C; D E S I R Study Group.
Fine-scale human genetic structure in Western France.
Eur J Hum Genet. 2015 Jun;23(6):831-6. doi: 10.1038/ejhg.2014.175. Epub 2014 Sep 3.


Béziau DM, Barc J, O'Hara T, Le Gloan L, Amarouch MY, Solnon A, Pavin D, Lecointe S, Bouillet P, Gourraud JB, Guicheney P, Denjoy I, Redon R, Mabo P, le Marec H, Loussouarn G, Kyndt F, Schott JJ, Probst V, Baró I.
Complex Brugada syndrome inheritance in a family harbouring compound SCN5A and CACNA1C mutations.
Basic Res Cardiol. 2014 Nov;109(6):446.


Lindenbaum P. and Redon R.
mod_bio: Apache modules for Next-Generation sequencing data
Bioinformatics. 2014 Sept 4. doi: 10.1093/bioinformatics/btu547

Bezzina CR, Barc J, Mizusawa Y, Remme CA, Gourraud JB, Simonet F, Verkerk AO, Schwartz PJ, Crotti L, Dagradi F, Guicheney P, Fressart V, Leenhardt A, Antzelevitch C, Bartkowiak S, Schulze-Bahr E, Zumhagen S, Behr ER, Bastiaenen R, Tfelt-Hansen J, Olesen MS, Kääb S, Beckmann BM, Weeke P, Watanabe H, Endo N, Minamino T, Horie M, Ohno S, Hasegawa K, Makita N, Nogami A, Shimizu W, Aiba T, Froguel P, Balkau B, Lantieri O, Torchio M, Wiese C, Weber D, Wolswinkel R, Coronel R, Boukens BJ, Bézieau S, Charpentier E, Chatel S, Despres A, Gros F, Kyndt F, Lecointe S, Lindenbaum P, Portero V, Violleau J, Gessler M, Tan HL, Roden DM, Christoffels VM, Le Marec H, Wilde AA, Probst V, Schott JJ, Dina C, Redon R.
Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death.
Nat Genet. 2013 Aug 28;45(9):1044-9. doi: 10.1038/ng.2712.
Acknowledgement

Riou R, Bressollette-Bodin C, Boutoille D, Gagne K, Rodallec A, Lefebvre M, Raffi F, Senitzer D, Imbert-Marcille BM, Retière C
Severe symptomatic primary HCMV infection despite effective innate and adaptive immune responses.
J Virol. 2016 Dec 28. pii: JVI.02245-16. doi: 10.1128/JVI.02245-16.

 

Leroy, T., Roux, C., Villate, L., Bodénès, C., Romiguier, J., Paiva, J. A., Kremer, A. .
Extensive recent secondary contacts between four European white oak species.
New Phytologist (2017).
 
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