Recherche

MEMM implements a Bayesian statistic method first presented in Klein et al. (2008). It estimates the pollen dispersal function and the variance in male fecundity on the basis of spatial information (positions of sampled plants, positions of all putative fathers in the study plot) and genetic information (genotypes of the sampled plants, putative fathers and sampled seeds).
Klein et al. (2011) investigates the performance of the method on simulated datasets and illustrate how neglecting the random component in male fecundity can lead to erroneous conclusions.

MIGALE a pour vocation de fournir des services à la communauté des sciences de la vie à travers quatre niveaux de service :

Mise à disposition d'une infrastructure informatique dédiée au traitement des données des sciences de la vie. Cette infrastructure comprend un cluster de calcul, des moyens de stockage, l'accès à des données publiques ou privées ainsi qu'à des outils bioinformatiques.

Diffusion d'un savoir-faire en informatique, bioinformatique et biostatistique par le biais de formations, de tutoriels, d'assistance et de conseil aux utilisateurs.

Conception et développement d'applications variées telles que des outils, des interfaces web conviviales et des bases de données.

Analyse de données génomiques, plus particulièrement à destination du métaprogramme MEM (Méta-omiques et Ecosystèmes Microbiens).

OntoBiotope Database is an on-line service for the navigation through the OntoBiotope database of microorganisms and habitats described in PubMed reference. The result of the user query is display through a treemap representation.

RCALI is a R package for CALculation of the Integrated flow of particles between polygons. It makes interface between CaliFloPP and R. CaliFloPP is a software that calculates flows of particles between pairs of polygons, when given a so-called individual dispersal function. The individual dispersal function describes the particle dispersion between pairs of points, and CaliFloPP deduces the total flows between pairs of polygons. Moreover, RCALI allows to take into account the angle of the current point with the horizontal, and so, to analyze anisotropic dispersal function.

Bibliothèque qui permet de définir un modèle générique couplant des EDP 2D pour modéliser la dynamique sur les parcelles bidimensionnelles et des EDP 1D pour la dynamique sur les éléments linéaires du paysage. Ce simulateur permet de résoudre ces modèles sur des paysages réalistes : paysages aléatoires ou réels représentés sous la forme d'objets géométriques 2D/1D. 

GMCPIC (Generalized Monte Carlo plug-in test with calibration) is an R-package implementing a computer intensive procedure to test the equality of two unknown vectors of probabilities p1 and p2 based on two multinomial draws performed with these probabilities. The GMCPIC package was specifically developed to test differences between pathogen compositions with small samples and sparse data.

SI scientifique basé sur une base de données sous PostgreSQL, dédiée au stockage des données d'observations de miellées et composé de plusieurs applications : visualisation de graphiques de calcul, récupération de données de la base, positionnement des ruchers sur une carte OSM, ... (détails concernant les applications dans les commentaires)

The allergy risk depends on the time of year, and, of course, on the presence of caterpillars.

The production of urticating setae begins during the larval stage "L3"  (Huchon and Démolin 1970). We begin by defining a potential allergy risk R0 which depends on the latitude and on the time of year, but which is independent on the presence of PPM. The computation of this potential allergy risk is based on the following assumptions :

1. There is a time t0, which corresponds to the beginning of the larval stage L3 and a time t1 which corresponds to the beginning of the procession. These times depend on the latitude only. They are computed on the basis of the chart in Démolin and Huchon (1970), adapted to the current geographical distribution of the PPM.

2. The duration of the procession is fixed to 30 days.

3. Urticating setae are released with a constant rate between t0 and t1, and with another (higher) rate during the procession.

4. The half-life of the setae is fixed to 10 days in the current version of the software.

Then, we define a function R1, which depends on the position (latitude, longitude), and roughly describes the distribution of the PPM nests:

5.  We build a map of the potential area of distribution of the PPM, using only the northern front and the altitudinal front in the Massif Central together with the altitudinal limit of 1400m.

6. Using the IGN map showing the location of pine trees, we restrict the area of distribution of the PPM to the locations where pine trees are present.

7. We use a smoothing kernel to take into account the uncertainty related with the presence of unlisted isolated host trees and PPM nests beyond the colonization front.

By overlaying maps R0 and R1, we obtain a model for the risk R as a function of position (latitude, longitude) and date.

pgs is a R package that can be used for computing and estimating the mean squared error of planar area and volume stereological estimators based on grids of points, lines, quadrats, serial sections, fakir beds...

Automatic generation of regular factorial designs, including fractional designs, orthogonal block designs, row-column designs and split-plots.

Creation, manipulation, simulation of linear Gaussian Bayesian networks from text files and more...

Agmial is an integrated system for bacterial genome annotation. It has been developed with the following requirements in mind :

• maximize annotation automation,
• ability to work on draft sequences,
• keep the program modular and extensible,
• choose informatics and bioinformatics standards when possible (e.g. Web Services, RDBMS, ...)
• distribute the program under an open-source license.

IGO (Integration from Genomes to Organisms) is a web portal that interconnects different online tools developed at MIG laboratory in various domains: Mosaic for the comparison of genomes, Prose for the protein sequences, Bacillus subtilis Expression Data Browser for the expression of B. Subtilis data, Pareo for metabolic pathways and Insyght for homologies/syntenies. The integration of the different web tools relies on passing arguments as URL parameters. The benefit of this approach is that web applications from different technological backgrounds can be interconnected without major additional development. However, the web tools must support URL parameters such as the organism name, the strain, the gene name or the locus tag. The IGO web interface has been developed using the Google Web Toolkit (GWT). Data are stored in a PostgreSQL relational database which currently contains 389 bacterial organisms.