WP7
Posted on octobre 7, 2010 by Olivier CollinCommentaires fermés sur WP7
Multiomics metadata infrastructure
Filed Under: Supplemental-material
ReNaBi
Posted on octobre 7, 2010 by Olivier CollinCommentaires fermés sur WP7
Multiomics metadata infrastructure
Filed Under: Supplemental-material
Posted on octobre 7, 2010 by Christophe BlanchetCommentaires fermés sur WP6
DistribOmics: Distributed infrastructure for omics
Filed Under: Supplemental-material
Posted on octobre 7, 2010 by Ivan MoszerCommentaires fermés sur WP5
WP5: Databases, Data Integration and Visualization
Database resources: comprehensive list.
Filed Under: Supplemental-material
Posted on octobre 7, 2010 by Vincent LefortCommentaires fermés sur WP4
Phylogeny and Comparative Genomics
ReNaBi’s platforms are developing algorithms for phylogenetic reconstruction (e.g. PhyML, Guindon et al. 2010) and tools for analyzing and viewing trees (e.g. TreeDyn or NJplot). These works are implemented in software applications that we distribute on the web; they may be downloaded and/or executed on-line. We also design integrated pipelines to compute multiple alignments, build trees and view the results in a user friendly environment (SeaView program, Gouy et al. 2010, and http://www.Phylogeny.fr/ web server, Dereeper et al. 2008). These programs and services are highly cited (PhyML >3,000 since original publication in 2003, SeaView >1,000 since original publication in 1996, cf. Web of Science) and widely used worldwide (Phylogeny.fr 10,000 analyses per month).
We are also working out phylo and comparative genomic databases, which are outstanding resources to elucidate the evolution and function of genes. HOVERGEN, HOGENOM and HOMOLENS (Penel et al. 2009, http://www.prabi.fr/) contain protein gene sequences clustered into groups of homologs. They integrate multiple sequence alignments and phylogenetic trees, and are regularly used for evolutionary studies (> 250 citations). GREENPHYLDB (Rouard et al. 2010) contains plant multigenic families and their associated orthology relationships derived from phylogenetic analyses. SOUTHGREEN provides a large panel of tools to analyze the genomes of tropical agronomy plants. All these databases are widely accessed (SOUTHGREEN 50,000 accesses per month, http://southgreen.cirad.fr/).
Filed Under: Supplemental-material
Posted on octobre 7, 2010 by Pierre TufféryCommentaires fermés sur WP3
WP3: Integration of structural bioinformatics services
Table1: Tools for Structural Bioinformatics developed by the partners of WP3.
Table2: Driving scientific projects, collaboration and services
Filed Under: Supplemental-material
Posted on octobre 7, 2010 by Yves VandenbrouckCommentaires fermés sur WP2
WP2: Proteomics and Metabolomics (supplemental material)
WP2.1:
WP2.2:
Table 1: Tools for Proteomics and Metabolomics developed by the partners of the WP2
Filed Under: Supplemental-material
Posted on octobre 4, 2010 by Christine GaspinCommentaires fermés sur WP1
NGS technologies:
Filed Under: Supplemental-material