PRABI-Doua

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

ProDom

Description

Protein domain database built with UniProt sequences. ProDom is part of the InterPro consortium.

Access conditions

Free online access.

Annual visits:
11 869 888 an
Unique visits:
22 180 an
Quotes:
231
Latest update:
25-03-2013

HOGENOM

Description

Homologous gene families database.

Access conditions

Free online access (http://doua.prabi.fr/databases/hogenom/).

Annual visits:
109 556 an
Unique visits:
Not documented
Quotes:
148
Latest update:
04-03-2015

PRIAM

Description

Enzyme-specific profiles for metabolic metabolic pathway prediction.

Access conditions

Free online access.

Annual visits:
154 145 an
Unique visits:
Not documented
Quotes:
94
Downloads:
Not documented

leBiBI

Description

Online system (associated with various sequence databases) devoted to bacterial taxonomic identification.

Access conditions

Free online access.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
3 066
Downloads:
21 450

SeaView

Description

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. Full description available from the software home page.

Access conditions

Freely downloadable software licensed under the GNU General Public Licence.

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

seqinR

Description

R library for sequence analysis. Full description available from the software home page.

Access conditions

Freely 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

ACNUC

Description

Sequence 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 conditions

Freely 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-4

Description

R library for multivariate analysis and graphical display. Full description available from the software home page.

Access conditions

Freely 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 phylogeny

Description

Training organized by CNRS Entreprises

Access conditions

Some knowledge in mathematics and statistics.

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
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 ... )

Organisation de plusieurs séminaires ou workshop chaque année.

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.

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