CBiB

Adress
146 Rue Léo Saignat 33076 Bordeaux
Structure(s)
Not documented
Unit:
Université de Bordeaux
Regional Center
IFB South West
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • CNOC (INRA)
  • ISO 9001
  • Label IBiSA
Infrastructure
Propriétaire
Effective storage
60.00 To
Cluster: cores number
96 cores
CPU/hours a year
87 600 H / an
Bioinformatic tools number
174
Users number (last year)
38
Servers description

Virtualization infrastructure

  • Cluster VMware
  • 2 servers DELL PowerEdge R905 (16 cores, 64 Go RAM)

Storage infrastructure

  • 1 storage based on ZFS for production, 50 TB (mirrored on remote site)
  • 1 NetApp appliance for production, 20 TB
  • 1 NetApp appliance for backup (remote site), 20 TB

Computing infrastructure

  • 1 computing server DELL PowerEdge R820 (32 cores, 512 Go RAM, 5 TB of space disk)
  • 1 computing server DELL PowerEdge R815 (32 cores, 256 Go RAM, 2.5 TB of space disk)
  • Galaxy portal, 1 server DELL PowerEdge R910 (32 cores/64 threads, 128 Go RAM, 800 GB of space disk)

Network infrastructure

  • Internet access 1 Gbits/s (shared)
  • LAN  10 Gbits/s
  • SAN FiberChannel 4 Gbits/s

Access conditions

Free account opening on demand (form to fill in).

Annual visits:
Not documented
Unique visits:
1 742 an
Quotes:
85
Latest update:
01-12-2015

Molligen

Description

Database dedicated to the comparative genomics of mollicutes

Access conditions

Free web access, a private access may be created

No website documented
Annual visits:
1 457 an
Unique visits:
564 an
Quotes:
23
Latest update:
01-10-2014

MeryB

Description

Web knowledgebase for the storage, visualisation, analysis and annotation of plant metabolomic profiles

Access conditions

Free web access, a private access may be created

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

Galaxy@CBiB

Description

Galaxy analysis server. Bioinformatics tools made available on the Toolshed: 400 tested bricks. 

Access conditions

Free web access, possibility of access to supplementary storage

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
24
Downloads:
Not documented

XEML-Lab

Description

Experiment metadata management

Access conditions

Free web access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
9
Downloads:
Not documented

Tango

Description

Metagenomics taxonomic assignment

Access conditions

Free web access.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
14
Downloads:
Not documented

MIX

Description

Finishing of genome assemblies

Access conditions

Free web access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
4
Downloads:
Not documented

xHeinz

Description

xHeinz  is a tool that finds provably optimal conserved active modules between two species.

Access conditions

Software website: https://software.cwi.nl/software/xheinz 

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

PepTeam

Description

PepTeam is a tool for biomarker discovery from the analysis of in-vivo screened repertoire of phage displayed libraries that has been sequenced by NGS.

Access conditions

Through CBiB Galaxy interface.

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

MICADo

Description

Mutation discovery in target PacBio cancer data with an alignment free method.

Access conditions

Public.

Domains of activity
  • Biomedical
  • Agri-food
  • Environment
  • Biology
Description of expertise domains

The goal of Bordeaux Bioinformatics Center (CBiB) is to design, implement and provide access to biological data analysis services suited to high speed production (eg., Genomics, proteomics, metabolomics, etc. .). This requirement to analyse large volumes of data quickly and reliably, brings the CBiB to develop "Big Data" specific methods. To do this, the CBiB meets the necessary skills in bioinformatics and computer science; the center is equipped with appropriate computing and storage means, consistent with regional facilities (the Mésocentre Calculation Aquitaine - CEC) and the National Bioinformatics Infrastructure (Investment Future, French Institute of Bioinformatics - IFB).

The CBiB structures its activities around three strategic areas:

 

1. NGS: Service activity for the treatment of data from New Sequencing Technologies. This axis developed in collaboration with the Platform Genome-Transcriptome Bordeaux, producer of data and with Genotoul Bioinformatics in Toulouse in the incipient collaboration ReNaBi / IBiSA (exchanges of expertise, sharing of training biologists, R & D missions).

​2. Comparative Genomics: research activity and service for the storage, analysis and large-scale comparison of bacterial genomes through the Molligen platform.

3. Metabolomics: In collaboration with the Metabolomics Platform Bordeaux (PMB) that produces the data, the CBiB is involved in data management projects in metabolomics with the recent extension of this work to eco-physiological data. Moreover, the CBiB is heavily involved in metabolomic data standardization activities at the European level (European COSMOS project).

​The Bordeaux Bioinformatics Center (CBiB) provides access to high performance computing resources, provides data analysis and features programming expertise. These resources are at the service of academic scientists and private companies to enable them to meet their needs in bioinformatics in an efficient and profitable manner.

Keywords:
  • NGS data analysis
  • Sequence analysis
  • Machine learning
  • System biology
  • Data curation
  • Ecology
  • Comparative genomics
  • Immunogenetics
  • Metabolomics and fluxomics
  • Proteomics

Formation professionnelle

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

Data mining and analysis of NGS data with R

Description
Not documented
Access conditions

CNRS fee-based training

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

Advanced sequence analysis

Description
Not documented
Access conditions

CNRS fee-based training

Trainees:
20 trainees / year
Training time:
6 day(s) / year
Upcoming session :
06-06-2017

Python for biology

Description
Not documented
Access conditions

CNRS fee-based training

Users distribution
International
15 %
National
5 %
Regional
12 %
Local
68%
Explanation about this distribution:

The given numbers correspond to people accessing the environement made available by the plateforme. The distribution is as following: INRA (18%), INSERM (9%), Bordeaux University (39%), industry (9%), CNRS (9%), international/others (16%).

Platform's own projects
(3)
  • MIX - Genome assembly finishing;
  • Tango - Taxonomic assignment (metagenomics);
  • MICADo - Mutation discovery in PacBio data;
 
Collaborations
National projets
(0)
Not documented
International and European projects
(2)
  • COBRA - Identification of plant factors involved in the virus infection cycle
  • COSMOS - Standards and data bases developpement
Projets with industry
(1)

Biodatacloud (Biogemma partner) - Developpement of a cloud computing system adapted to NGS data analysis

Collaboration projects not founded through an external organism
(14)
  • 16S  Metagenomics analysis (Service de rhumatologie CHU Bordeaux)
  • Bioinformatics methods for analyzing resistance to antihormonal treatments for breast cancer (Unité INSERM ACTION Equipe cancer du sein, Institut Bergonié Bordeaux)

  • New methods of acquisition and classification for high content screening of membrane receptor organization and dynamics using super-resolution microscopy (Institut interdisciplinaire de Neurosciences CNRS UMR 5297)
  • Development of a database and an interface for the migration, the perpetuation and use of the Metabolic database PLATO (UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux Aquitaine)
  • Diversity of viral sequences in HIV-infected patients (Laboratoire de Virologie UMR 5234, Université Bordeaux)

  • Vitis Riparia genome assembly (UMR 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, ISVV Bordeaux)
  • Analysis of NGS data of variable chains of human immunoglobulin genes selected by phage display in vivo for targeting atheroma plaque (Résonance Magnétique des Systèmes Biologiques, UMR 5536 CNRS / Université de Bordeaux)
  • Implementation of bioinformatics tools for strawberries: Investigation of the number of mutations in two EMS mutants, Assembly of de novo sequences in the polyploid strawberry (UMR 1332 Biologie du Fruit et Pathologie)
  • Analysis of 40 exomes from apocrine molecular tumors (ACTION U1218, Equipe cancer du sein – Institut Bergonié)
  • Transcriptome analysis for 594 sarcomas (ACTION U1218, Equipe Sarcome - Institut Bergonié)
  • Studies of the mechanisms involved in the resistance of NB4 and NB4R1 cells to ATRA (Institut Bergonié)
  • DypFISH: analysis of co-localization of RNA and proteins at sub-cellular resolution (Faculty of Health Sciences, Department of Integrative Biomedical Sciences, University of Cape Town)

  • UmLiLo - Search for conserved patterns and variations in non-coding RNAs (Faculty of Health Sciences, Department of Integrative Biomedical Sciences, University of Cape Town)
  • Storage of NGS data from highly similar genomes (LaBRI Université de Bordeaux et UMR 1332 Biologie du Fruit et Pathologie - INRA / Université de Bordeaux)
Provision of services not founded through an external organism
(3)
Compost metagenomics analysis IFPEN (Institut Français du Pétrole et des Énergies Nouvelles); Gliom RNA-Seq data analysis (INSERM U1029 LAMC, Université de Bordeaux); Development of an analysis pipeline for proteomics data meant to identify novel protein markers for hepatocellular adenoma (Bariton INSERM U1053 Cytoskeleton and Cancer, Université de Bordeaux);
Animations (Workshops, Work-groups, seminars, conferences ... )

In collaboration with the SVS department of the University of Bordeaux, IFB and France Génomique, CBiB organized 4 «2-in-1 Workshops»: Production and Analysis of NGS data (80 participants on average at each workshop )

  • RNA-Seq, 22 avril 2016.
  • Whole genome, 3 mai 2016
  • Exomes and gene panels, 20 septembre 2016
  • Metagenomics, 7 novembre 2016
Internal publications

Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, et al.. MICADo - Looking for mutations in targeted PacBio cancer data: an alignment-free method. Frontiers in Genetics, Frontiers, 2016


Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus Dittrich, Tobias Muller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, and Gunnar W. Klau. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, 31(19), 2015. doi: 10.1093/bioinformatics/btv316.


Thomas Hume, Hayssam Soueidan, Macha Nikolski, and Guillaume Blin. Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem. In Giuseppe F. Italiano, editor, 41st International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM’15), volume 8939, pages pp. 242–253, Pecpod Snezkou, Czech Republic, January 2015. LNCS.


Hayssam Soueidan, Louise-Amelie Schmitt, Thierry Candresse, and Macha Nikolski. Finding and identifying the viral needle in the metagenomic haystack: Trends and Challenges. Frontiers in Microbiology, page 5:739, December 2014. doi: 10.3389/fmicb.2014.00739


Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, and Macha Nikolski. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics, October 2013. doi:10.1186/1471–2105–14–S15–S16


Thomas Hume, Hayssam Soueidan, V. Fabienne Wong Jun Tai, Antoine Vekris, Klaus Petry, and Macha Nikolski. Efficient mapping of short peptides on whole proteome database for biomarker discovery. In JOBIM 2013, France, July 2013.

External publications

Senta Heiss-Blanquet, Françoise Fayolle-Guichard, Vincent Lombard, Agnès A. Hebert, Pedro Coutinho, Alexis Groppi, Aurélien Barré, and Bernard Henrissat. Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures. PLoS ONE, December 2016. doi: 10.1371/journal.pone.0167216.


Géraldine Gourgues, Aurélien Barré, Emmanuel Beaudoing, Johann Weber, Ghislaine Magdelenat, Val´erie Barbe, Elise Schieck, Joerg Jores, Sanjay Vashee, Alain Blanchard, Carole Lartigue, and Pascal Sirand-Pugnet. Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia. Genome Announcements, 4(2), April 2016. doi: 10.1128/genomeA.00263-16. 


Yves Gleize, Fanny Mendisco, Marie-Hélène Pemonge, Christophe Hubert, Alexis Groppi, Bertrand Houix, Marie-France Deguilloux, and Jean-Yves Breuil. Early Medieval Muslim Graves in France: First Archaeological, Anthropological and Palaeogenomic Evidence. PLoS ONE, February 2016. doi: 10.1371/journal.pone.0148583. 


Eric Dausse, Aurélien Barré, Aimé Ahissan, Alexis Groppi, Alain Rico, Ainali Chrysanthi, Gilmar Sal- gado, William Palau, Emilie Daguerre, Macha Nikolski, Jean-Jacques Toulmé, and Carmelo Di Primo. Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation. Biosen- sors and Bioelectronics, February 2016.


Yvan Le Bras, Olivier Collin, Cyril MONJEAUD, Vincent Lacroix, Eric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru, and Pierre Peterlongo. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. Gi- gaScience, 5(1), February 2016. doi: 10.1186/s13742-015-0105-2. 


A-F Adam-Blondon, M Alaux, C Pommier, D Cantu, Z-M Cheng, GR Cramer, C Davies, S Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell, JP Londo, P Kersey, F Mattivi, S Naithani, P Neveu, M Nikolski, M Pezzotti, BI Reisch, R Töpfer, MA Vivier, D Ware, and H Quesneville. Towards an open grapevine information system. Horticulture research, 2016. doi: 10.1038/hortres.2016.56.


Gaetan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, and Guillaume Rizk. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics, 16(1), September 2015. doi: 10.1186/s12859- 015-0709-7.


Stephanie Mariette, V. Fabienne Wong Jun Tai, Guillaume Roch, Barre Aurelien, Chague Aurelie, Decroocq Stephane, Groppi Alexis, Laizet Yec’han, Lambert Patrick, Tricon David, Nikolski Macha, Audergon Jean-Marc, Abbott Albert G., and Decroocq Veronique. Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytol- ogist,  page  DOI:  10.1111/nph.13627,  September  2015. doi: 10.1111/nph.13627


Nathalie Quenel-Tueux, Marc Debled, Justine Rudewicz, Gaetan Macgrogan, Marina Pulido, Louis Mauriac, Florence Dalenc, Thomas Bachelot, Lortal Barbara, Christelle Breton-Callu, Nicolas Madranges, Christine Tunon De Lara, Marion Fournier, Herve Bonnefoi, Hayssam Soueidan, Macha Nikolski, Audrey Gros, Daly Catherine, Wood Henry, Rabbitts Pamela, and Richard Iggo. Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in post- menopausal patients treated for large operable or locally advanced hormone-receptor-positive breast cancer. British Journal of Cancer, page bjc.2015.247, July 2015. doi: 10.1038/bjc.2015.247. 


Reza M. Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo Reijmers, Antonio Rosato, Leonardo Tenori, Paola Turano, Silvia Marin, Catherine Deborde, Daniel Jacob, Dominique Rolin, Benjamin Dartigues, Pablo Conesa, Kenneth Haug, Philippe Rocca-Serra, Steve O’Hagan, Jie J. Hao, Michael van Vliet, Marko Sysi-Aho, Christian Ludwig, Jildau Bouwman, Marta Cascante, Timothy Ebbels, Julian L. Griffin, Annick Moing, Macha Nikolski, Matej Oresic, Susanna-Assunta Sansone, Mark R. Viant, Royston Goodacre, Ulrich L. Gunther, Thomas Hankemeier, Claudio Luchinat, Dirk Walther, and Christoph Steinbeck. CO- ordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics, page Journal no. 11306, May 2015. doi: 10.1007/s11306-015-0810-y. 


Raluca Uricaru, Celia Michotey, Helène Chiapello, and Eric Rivals. YOC, A new strategy for pairwise alignment of collinear genomes. BMC Bioinformatics, 16:16:111, April 2015. doi: 10.1186/s12859- 015-0530-3. 


Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Elon Correa, Saravanan Dayalan, Alejandra Gonzalez-Beltran, Tim Ebbels, Royston Goodacre, Janna Hastings, Kenneth Haug, Albert Koulman, Macha Nikolski, Matej Oresic, Susanna-Assunta Sansone, Daniel Schober, James Smith, Christoph Steinbeck, Mark R. Viant, and Steffen Neumann. Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics, 2015. doi: 10.1007/s11306-015-0879-3. 


Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi, Claire Lemaitre, and Pierre Peterlongo. Reference-free detection of isolated SNPs. Nucleic Acids Research, pages 1 – 12, November 2014. doi: 10.1093/nar/gku1187.


Richard Iggo, Justine Rudewicz, Elodie Monceau, Nicolas Sevenet, Jonas Bergh, Tobias Sjoblom, and Herve Bonnefoi. Validation of a yeast functional assay for p53 mutations using clonal sequencing. Journal of Pathology, 231(4):441–8, December 2013. doi: 10.1002/path.4243.


David Benaben, Catherine Biscarat, Yonny Cardenas, Helene Cordier, Pierre Gay, Benoit Hiroux, Gilles Mathieu, Jean Yves Nief, and Jerome Pansanel. Mise en place d’un gestionnaire de donnees leger, pluridisciplinaire et national pour les données scientifiques. In Journees SUCCES 2013, Paris, France, November 2013.


Macha Nikolski, Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, and Gabriel Valiente. Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinformatics, August 2013. doi: 10.1093/bioinformatics/btt256.


Emilie Dordet-Frisoni, Eric Baranowski, Aurelien Barre, Alain Blanchard, Marc Breton, Carole Cou- ture, Virginie Dupuy, Patrice Gaurivaud, Daniel Jacob, Claire Lemaitre, Lucıa Manso-Silvan, Macha Nikolski, Laurent-Xavier Nouvel, Francois Poumarat, Pascal Sirand-Pugnet, Patricia Thebault, Sébastien Theil, Francois Thiaucourt, Christine Citti, and Florence Tardy. Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae. Genome Announcements, 1(3):epub ahead of print, 2013. doi: 10.1128/genomeA.00280-13.


Virginie Dupuy, Pascal Sirand-Pugnet, Eric Baranowski, Aurelien Barre, Marc Breton, Carole Couture, Emilie Dordet-Frisoni, Patrice Gaurivaud, Daniel Jacob, Claire Lemaitre, Lucıa Manso-Silvan, Macha Nikolski, Laurent-Xavier Nouvel, Fran ̧cois Poumarat, Florence Tardy, Patricia Thebault, Sebastien Theil, Christine Citti, Alain Blanchard, and Francois Thiaucourt. Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats. Genome Announcements, 1(3):e00354–13, 2013. doi: 10.1128/genomeA.00354-13.


Lucıa Manso-Silvan, Florence Tardy, Eric Baranowski, Aurelien Barre, Alain Blanchard, Marc Breton, Carole Couture, Christine Citti, Emilie Dordet-Frisoni, Virginie Dupuy, Patrice Gaurivaud, Daniel Jacob, Claire Lemaitre, Macha Nikolski, Laurent-Xavier Nouvel, Francois Poumarat, Patricia Thebault, Sebastien Theil, Francois Thiaucourt, and Pascal Sirand-Pugnet. Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle. Genome Announcements, 1(3):e00348–13, 2013. doi: 10.1128/genomeA.00348-13

Publications with the hosting laboratory

Jonathan Dubois, Amine Ghozlane, Patricia Thebault, Isabelle Dutour, and Romain Bourqui. Genome-wide detection of sRNA targets with rNAV. In Symposium on Biological Data Visualization, United States, October 2013.


Jonathan Dubois, Ludovic Cottret, Amine Ghozlane, David Auber, Frederic Bringaud, Patricia Thebault, Fabien Jourdan, and Romain Bourqui. Visualization of time-series data in the context of metabolic networks with Systrip Software. In Journees Ouvertes Biologie Informatique Mathematiques (JOBIM 2013), France, July 2013.

Development
Le CBiB a déposé auprès de l’Agence pour la Protection des Programmes (APP) une application de gestion de données métabolomiques (MetaboP) N° IDDN.FR.001.160001.000.S.P.2008.000.10300.
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