Archive for octobre, 2010

WP7

Posted on octobre 7, 2010 by Commentaires fermés sur WP7

Multiomics metadata infrastructure

Filed Under: Supplemental-material

WP6

Posted on octobre 7, 2010 by Commentaires fermés sur WP6

DistribOmics: Distributed infrastructure for omics

Filed Under: Supplemental-material

WP5

Posted on octobre 7, 2010 by Commentaires fermés sur WP5

WP5: Databases, Data Integration and Visualization

Database resources: comprehensive list.

Filed Under: Supplemental-material

WP4

Posted on octobre 7, 2010 by Commentaires 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

WP3

Posted on octobre 7, 2010 by Commentaires 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

WP2

Posted on octobre 7, 2010 by Commentaires fermés sur WP2

WP2: Proteomics and Metabolomics (supplemental material)

WP2.1:

Figure 1: Functional components of the integrated software architecture for proteomics and metabolomics

WP2.2:

Table 1: Tools for Proteomics and Metabolomics developed by the partners of the WP2

Filed Under: Supplemental-material

WP1

Posted on octobre 4, 2010 by Commentaires fermés sur WP1

NGS technologies:

Filed Under: Supplemental-material