PRABI-Lyon-Grenoble
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
43 boulevard du 11 Novembre 1918
Université Claude Bernard – Lyon 1 69622 Villeurbanne
Structure(s)
CNRS
Unit:
LBBE, UMR 5558
Website
PRABI-DouaScientific leader(s)
Technical leader(s)
Technical leader
Not documentedCertificat(s)
Not documented
Team
- Perrière Guy
- Boussau Bastien
- Brochier Armanet Céline
- Charles Hubert
- Daubin Vincent
- De Vienne Damien
- Dray Stéphane
- Duret Laurent
- Fey Jonathan
- Flandrois Jean Pierre
- Fournier Amandine
- Gouy Manolo
- Gueguen Laurent
- Jacob Laurent
- Kahn Daniel
- Lacroix Vincent
- Lartillot Nicolas
- Lerat Emmanuelle
- Marais Gabriel
- Mary Arnaud
- Miele Vincent
- Penel Simon
- Picard Franck
- Sagot Marie France
- Siberchicot Aurélie
- Sinaimeri Blerina
- Tannier Eric
- Thioulouse Jean
- Veber Philippe
Infrastructure
Propriétaire
Effective storage
515.00 To
Cluster: cores number
1 032 cores
Data collections number
10
CPU/hours a year
3 850 000 H / an
Bioinformatic tools number
120
Users number (last year)
150
Servers description
One task submission server: Dell PowerEdge R630, 2 Intel Xeon E5-2650 v3 (10 cores/20 threads), 96 Gb RAM.
One scheduling server: VM Intel 5430 with 3 CPUs and 8 Gb RAM.
Access conditions
Scientific collaboration with PRABI-Doua or LBBE
Annual visits: 160 000 an
Unique visits: Not documented
Quotes: 800
Latest update: 01-12-2015
ProDomDescriptionProtein domain database built with UniProt sequences. ProDom is part of the InterPro consortium. Access conditionsFree online access. |
Annual visits: 11 869 888 an
Unique visits: 22 180 an
Quotes: 231
Latest update: 25-03-2013
HOGENOMDescriptionHomologous gene families database. Access conditionsFree online access (http://doua.prabi.fr/databases/hogenom/). |
Annual visits: 109 556 an
Unique visits: Not documented
Quotes: 148
Latest update: 04-03-2015
PRIAMDescriptionEnzyme-specific profiles for metabolic metabolic pathway prediction. Access conditionsFree online access. |
Annual visits: 154 145 an
Unique visits: Not documented
Quotes: 94
Downloads: Not documented
leBiBIDescriptionOnline system (associated with various sequence databases) devoted to bacterial taxonomic identification. Access conditionsFree online access. |
Annual visits: Not documented
Unique visits: Not documented
Quotes: 3 066
Downloads: 21 450
SeaViewDescriptionSeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. Full description available from the software home page. Access conditionsFreely downloadable software licensed under the GNU General Public Licence. |
Annual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
seqinRDescriptionR library for sequence analysis. Full description available from the software home page. Access conditionsFreely available for download from any CRAN (Comprehensive R Archive Network) mirror. |
Annual visits: Not documented
Unique visits: Not documented
Quotes: 1 350
Downloads: Not documented
ACNUCDescriptionSequence retrieval system for the nucleotide (GenBank, EMBL) and protein (UniProt) sequence databases and for many other systems following the same formats. Full description available froim the software home page. Access conditionsFreely downloadable software licensed under the GNU General Public License (http://doua.prabi.fr/databases/acnuc) or on-line access through a web interafce (http://doua.prabi.fr/search/query_fam). |
Annual visits: Not documented
Unique visits: Not documented
Quotes: 1 993
Downloads: Not documented
ADE-4DescriptionR library for multivariate analysis and graphical display. Full description available from the software home page. Access conditionsFreely available for download from any CRAN mirror. |
Domains of activity
- Biomedical
- Agri-food
- Environment
- Biology
Description of expertise domains
Les thématiques de recherche du PRABI-Doua s’organisent autour d’un point de vue méthodologique, qui affirme l’importance de la modélisation tant mathématique qu’informatique et d’une perspective évolutive qui organise les recherches indépendamment du niveau d’organisation biologique. C’est dans la synergie entre des problématiques biologiques propres et des développements méthodologiques que naît la plus grande part des résultats scientifiques de cette composante. Parmi les thématiques abordées figurent en particulier:
- Phylogénie et évolution moléculaire.
- Génomique comparative (organismes eucaryotes et procaryotes).
- Eléments transposables.
- Intreractions hôtes-parasites.
- Statistiques appliquées à l'écologie et l'évolution.
- Analyse statistique de données en grandes dimensions pour la génomique.
Keywords:
- Sequence analysis
- Sequence algorithmics
- Biostatistics
- Descriptive statistics
- Statistical tests
- Regression
- Multivariate analysis
- Dimension reduction
- Inferences and biological network analysis
- Information and communication technology developments
- Tools
- Interfaces, web portals
- Workflows developments
- Data
- Databases and information systems
- Computing environments
- Cluster
- Cloud
- Ecology
- Population genetics
- Biodiversity
- Microbial ecology
- Modelling in ecology
- Molecular evolution
- Genes and genomes
- Speciation dating
- Phylogenomics
- Tree of life
- Supertrees et reconciliations
- Selection detection
- Comparative genomics
- Genome comparison
Formation professionnelle
Trainees: 8 trainees / year
Training time: 4 day(s) / year
No upcoming session scheduled
Introduction to molecular phylogenyDescriptionTraining organized by CNRS Entreprises Access conditionsSome knowledge in mathematics and statistics. |
Internal publications
External publications
Publications with the hosting laboratory
Berthoumieux, S., Brilli, M., Kahn, D., de Jong, H. and Cinquemani, E. (2013) On the identifiability of metabolic network models. J. Math. Biol., 67, 1795-1832.
Bernard, E., Jacob, L., Mairal, J. and Vert, J.P. (2014) Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. Bioinformatics, 30, 2447-2455.
Frenkel-Morgenstern, M., Gorohovski, A., Lacroix, V., Rogers, M., Ibanez, K., Boullosa, C., Andres Leon, E., Ben-Hur, A. and Valencia, A. (2013) ChiTaRS: a database of human mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res., 41, D142-151.
Kim, S.Y., Jacob, L. and Speed, T.P. (2014) Combining calls from multiple somatic mutation-callers. BMC Bioinformatics, 15, 154.
Rajaraman, A., Tannier, E. and Chauve, C. (2013) FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics, 29, 2987-2994.
Mirarab, S., Bayzid, M.S., Boussau, B. and Warnow, T. (2014) Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science, 346, 1250463.
Uricaru, R., Rizk, G., Lacroix, V., Quillery, E., Plantard, O., Chikhi, R., Lemaitre, C. and Peterlongo, P. (2014) Reference-free detection of isolated SNPs. Nucleic Acids Res., 43, e11.
Sjostrand, J., Tofigh, A., Daubin, V., Arvestad, L., Sennblad, B. and Lagergren, J. (2014) A Bayesian method for analyzing lateral gene transfer. Syst. Biol., 63, 409-420.
Flandrois, J.P., Perrière, G. and Gouy, M. (2015) leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics, 16, 251.
Anselmetti, Y., Berry, V., Chauve, C., Chateau, A., Tannier, E. and Berard, S. (2015) Ancestral gene synteny reconstruction improves extant species scaffolding. BMC genomics, 16(Suppl. 10), S11.
Baudet, C., Donati, B., Sinaimeri, B., Crescenzi, P., Gautier, C., Matias, C. and Sagot, M.F. (2015) Cophylogeny Reconstruction via an Approximate Bayesian Computation. Syst. Biol., 64, 416-431.
Biller, P., Guéguen, L. and Tannier, E. (2015) Moments of genome evolution by Double Cut-and-Join. BMC Bioinformatics, 16(Suppl. 14), S7.
Semeria, M., Tannier, E. and Guéguen, L. (2015) Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies. BMC Bioinformatics, 16(Suppl. 14), S5.
Szöllosi, G.J., Tannier, E., Daubin, V. and Boussau, B. (2015) The inference of gene trees with species trees. Syst. Biol., 64, e42-62.
Donati, B., Baudet, C., Sinaimeri, B., Crescenzi, P. and Sagot, M.F. (2015) EUCALYPT: efficient tree reconciliation enumerator. Algo. Mol. Biol., 10, 3.
Bosi, E., Donati, B., Galardini, M., Brunetti, S., Sagot, M.F., Lio, P., Crescenzi, P., Fani, R. and Fondi, M. (2015) MEDUSA: a multi-draft based scaffolder. Bioinformatics, 31, 2443-2451.
Dray, S. and Josse, J. (2015) Principal component analysis with missing values: a comparative survey of methods. Plant Ecol., 216, 657-667.
Dray, S., Pavoine, S. and Aguirre de Carcer, D. (2015) Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA). Mol. Ecol. Resour., 15, 242-249.
Users distribution
International
0 %
National
0 %
Regional
15 %
Local
85%
Explanation about this distribution:
Les seuls services proposés par la composante PRABI-Doua correspondent aux service en ligne (accès aux banques de données, recherche de similarités, identification taxonomique, téléchargement de logiciels, etc.) ce qui explique le caractère international de l’accès.
Platform's own projects
Une vingtaine de logiciels développés et maintenus
Collaborations
National projets
En moyenne 4 par an.
International and European projects
Un ERC.
Projects with industry
Collaboration projects not founded through an external organism
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Organisation de plusieurs séminaires ou workshop chaque année.
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