Agmial est une chaîne d'annotation de génomes bactériens qui s'appuie sur un certain nombre d'outils développés au laboratoire (SHOW, Prose, Pareo, ...). Agmial n'est plus maintenu, mais a permis l'annotation de plus de 300 génomes bactériens.

BioYaTeA is an extension of the YaTeA term extractor that deals with prepositional attachments and adjectival participle. It extracts terms from documents in French and in Eglish. Its distribution includes post-filtering of irrelevant terms. It is publicly available as CPAN module. Part of this work has been funded by the European project Alvis and the French project Quaero. See (Golik et al., CiCLING'2013) for more details.

GGMselect is a R package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.

IDEAS is a Matlab^®  toolbox for parameter identification of ordinary differential equation (ODE) models.  The parameter estimation is performed in the maximum-likelihood (ML) sense. IDEAS offers several options for the optimal criterion, depending on the hypothesis on the covariance matrix of the measurement errors.
The main feature of IDEAS is the assessment of the uncertainty of the estimates, based on the symbolic computation of sensitivity functions to evaluate the Fisher information matrix.

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.

nls2 is a set of R functions and programs to estimate the parameters of a non-linear regression model over a given set of observations.

The regression function can be defined explicitly as a function of independent variables and of unknown parameters or it can be defined as the solution of a system of differential equations. Heteroscedasticity of errors can be taken into account by modelling the variance function.

Several additional tools are included: plotting functions, functions to process series of estimations, calculate confidence intervals and confidence regions for parameters and functions of parameters, and process calibration study. The description of the models can be provided by using a symbolic syntax.

Cet outil permet d'obtenir un ensemble cohérent de paramètres pour un modèle métabolique cinétique. En utilisant des données expérimentales de façon aveugle, on risque d'obtenir un jeu de paramètres incomplet et/ou incohérent. Grâce à cet outil, les paramètres calculés à partir des données respectent certaines contraintes physiques et appartiennent à des gammes connues de paramètres biochimiques. L’outil est directement utilisable en ligne, son code (Python et Matlab) est également disponible.

Package R which computes sensitivity indexes by using a method based on a truncated Polynomial Chaos Expansion of the response and regression PLS, for computer models with correlated continuous inputs, whatever the input distribution. The truncated Polynomial Chaos Expansion is built from the multivariate Legendre orthogonal polynomials.
 The number of runs (rows) can be smaller than the number of monomials. It is possible to select only the most significant monomials.
 Of course, this package can also be used if the inputs are independent. Note that, when they are  independent and uniformly distributed, the package 'polychaosbasics' is more appropriate.

Package R which computes sensitivity indexes by using a method based on a truncated Polynomial Chaos Expansions of the response.
 The necessary condition of the method is: the inputs must be uniformly and independently sampled. Since the inputs are uniformly distributed, the truncated Polynomial Chaos Expansion is built from the multivariate Legendre orthogonal polynomials.

R-package for Multidimensional Numerical Integration.

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/.

RCALI is a R package that 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.

Le format de données SBtab contient un ensemble de conventions pour le traitement de données en biologie des systèmes. Son objectif est de simplifier l’échange de données par des noms et des annotations standardisés. Un outil de validation et de conversion au format SBML, ainsi que le code en Python, Matlab et R, sont disponibles en ligne.

Indices de sensibilité avec entrées corrélées dépendantes calculés avec une méthode basée sur les VIP de la régression PLS.
Le R package sivipm calcule les indices de sensibilité totaux et individuels, les composantes significatives, et l'intervalle de confiance des indices de sensibilité totaux. Les indices de sensibilité sont calculés par  une méthode proposée par  J.P. Gauchi, basée sur les VIP de la régression PLS. Les composantes significatives sont déterminées par la règle du logiciel SIMCA et par le test de Lazraq &  Cléroux. Les intervalles de confiance sont calculés par la méthode bootstrap.