Recherche

LINselect is a R package which allows to estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.

R2Cuba is a R package which implements four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre. It is a wrapper around the Cuba-1.6 library by Thomas Hahn available from the URL http://www.feynarts.de/cuba/.

CompaGB (http://genome.jouy.inra.fr/CompaGB) helps the scientific community to

(1) choose a genome browser that would better fit their particular project,

(2) visualize features comparatively with easily accessible formats, such as tables or radar plots and

(3) perform their own evaluation against the defined criteria.

It is an open project, anyone in the community can perform new evaluations as well as concurrent evaluations of already evaluated softwares.

At the beginning of this project we came to the conclusion that we wouldn’t be able to meet the requirement of 3 critical factors:

(1) having a exhaustive number of softwares evaluated,

(2) having evaluations up to date with software’s releases and

(3) providing a broad representation of the views from the different communities of users. Our answer to this was to make CompaGB an open framework in which anyone interested can participate.

The development of this package was led by the idea that it is a bad practice to separate code and documentation. Code and documentation should be at the same place so that both can easily be modified simultaneously. We proceed according to this principle since the middle of the 90ties using a Perl script (a very convenient language for this kind of tasks). Now, we share it with the community by the more convenient way of an R package. The recent development of R make things quite easy.

To use documair, each code defining an object (either function or variable) must be encapsulated within a series of tagged comments; we propose tags but their values can be adapted as you wish (by modifying the ‘documair0$tag$v’ list). From these tagged comments, documair automatically writes ‘Rd’ files and gathers them with a few more files to produce the complete package until the ‘tar.gz’. For some specific objects, the user can write manually the ‘Rd’ file. All the necessary files must be gathered in a unique directory. In it, the user must place the following set of mandatory files (in the following ‘pkg’ will designate the name of the package) :

1. A ‘pkg.DESCRIPTION’ file: the standard text DESCRIPTION file to be associated to the pack-age. The NAMESPACE file is automatically created from the exported objects and the pres-ence of C and Fortran files.

2. A ‘pkg.package.Rd’ file: a text file describing in Rd syntax the general description of the package to appear in the documentation. This file can be slightly supplemented by documair to add some additional information.

3. As many as wanted ‘foo.code.r’ files where are placed the documented code of each object. Each files can include more than one object. The extension ‘code.r’ can be modified within the ‘pkg.which.txt’ file.

We propose two least-squares estimators of a discrete probability under the constraint of k-monotony and study their statistical properties. We give a characterization of these estimators based on the decomposition on a spline basis of k-monotone sequences. We develop an algorithm derived from the Support Reduction Algorithm and we finally present a simulation study to illustrate their properties.

The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query, a list of structural neighbors and their alignments are provided. DOMIRE, by displaying the protein structural domain organization, can be a useful tool for defining protein common cores and for unravelling the evolutionary relationship between different proteins.

FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data :

(i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and

(ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model.

G-protein-coupled receptors (GPCRs) form the largest class of membrane proteins and represents the largest gene family, accounting for 3 to 5% of the mammalian genome. They are key components of several cellular response mechanisms to environmental signals. The first experimental three-dimensional (3D) structure, the bovine rhodopsin, was solved in 2000. Since then, our knowledge about GPCR structures has expanded with the release of more than thirty new 3D structures. However, olfactory receptor structures are still missing calling for the use of homology modeling techniques. GPCRautomodel aims at narrowing the gap between known structures and receptors of interest to the biologists. Its primary focus is the high-throughput modeling of GPCR proteins and the subsequent docking of putative ligands. The current version of GPCR automodel can potentially be employed to model any GPCR and its interaction with a molecule of interest for the user. The results are displayed in a user friendly web interface. Its update is currently in progress and should be released soon.

The S. aureus Expression Data Browser contains summarised information of tiling array log2-expression data in different growth conditions (Highest Expression Conditions, Most Positively Correlated Segments, Expression Profile, Annotation, Genomic View of Gene/Segment, ...) acquired for S. aureus.

LiTe is a C++ library devoted to planar Gibbsian T-tessellations. It is a software companion of the paper "A completely random T-tessellation model and Gibbsian extensions" published in Spatial Statistics 2013, vol. 6 (preliminary version freely available on HAL and arXiv). Note that LiTe is also available to R users, as the RLiTe package (http://kien-kieu.github.io/lite/rlite.html). Using LiTe, one can

• Perform some basic operations on T-tessellations.
• Define a Gibbs model of T-tessellations.
• Simulate a given Gibbs model of T-tessellations.
• Estimate the parameters of a given model.

LiTe stands for Line Tessellation. By line tessellation, we mean tessellations that are built upon a line pattern rather than a point pattern. Examples of point tessellations are Voronoi and Laguerre tessellations. A T-tessellation is only a special case of line tessellation. Other types of line tessellations may be supported in LiTe in the future.

In addition to the reference manual documenting classes and their members, specific documentation topics are provided.

LiTe relies heavily on CGAL, the Computational Geometry Algorithms Library. By using CGAL data structures and algorithms, LiTe developers saved a lot of time and effort. The slight drawback of using CGAL is that LiTe depends on a third-party library that must be installed separately by LiTe users. Fortunately, CGAL has many users working in diverse computing environments (hardware, OS, compiler). Therefore CGAL installation is largely tested and documented.

modèle de mélange pour graphes valués, sous Matlab

This projet aims at identifying the genetic basis of wine yeasts fermentation traits. It combines a classical QTL approach with a gene expression study between an industrial wine yeast strain (EC1118) derivative (59A) and the laboratory yeast strain (S288C). Information produced during this project (SNP, QTL, eQTL...) are accessible on the Genome Browser using the 'Select Tracks' tab.

The GEMO database includes the genomes of eight strains of the species M. oryzae representing different genetic groups pathogenic of different species of Poacees and one strain of the sister species M. grisea.

FisPro (Fuzzy Inference System Professional) permet de créer des systèmes d'inférence floue (SIF), et de les utiliser à des fins de raisonnement, en particulier pour la simulation d'un système physique ou biologique. Les systèmes d'inférence floue sont décrits brièvement dans le glossaire de logique floue donné dans la documentation de l'utilisateur. Ils fonctionnent à partir de règles de raisonnement floues, qui ont l'avantage de gérer la progressivité des phénomènes. La logique floue, depuis les premiers travaux de Zadeh, s'est révélée comme une puissante interface entre espaces symboliques et numériques. L'une des raisons en est la capacité des systèmes flous à incorporer des connaissances expertes et leurs nuances, et la possibilité d'exprimer le comportement d'un système en termes interprétables. Une autre raison est la possibilité de concevoir des systèmes par apprentissage à partir de données afin de tirer le meilleur parti de celles-ci. 

Ce logiciel est formé de deux parties distinctes : une bibliothèque de fonctions, écrite en C++, qui peut être utilisée de manière autonome et une interface utilisateur, écrite en Java, qui en implémente les principales fonctionnalités. Portable, il peut s'exécuter sur la majorité des plates-formes informatiques existantes. 

voir la présentation