Section: New Software and Platforms

Upgraded Software

NIMROD

We have written a specific program called NIMROD for estimating parameter of ODE based population models. It has been regularly updated. For instance, we have adapted the program for parallel computing, in collaboration with the MCIA (Mésocentre de calcul intensif Aquitain) facility, which makes available a large computer with more than 3000 cores. This program is described in [43] . Although the program is available on the ISPED website (http://etudes.isped.u-bordeaux2.fr/BIOSTATISTIQUE/NIMROD/documentation/html/index.html .), it is not user-friendly and needs further improvement to be more widely used. By now, the users are the current or previous (Jérémie Guedj, Julia Drylewicz, Mélanie Prague) members of the team and close collaborators (Andrew Yates). Furthermore, as a validation step, it would need a head-to-head comparison with other available softwares. We bet that our program can be very competitive for parameter identification in ODE models with more than two compartments.

marqLevAlg

An R package for function optimization. Available on CRAN, this package performs a minimization of function based on the Marquardt-Levenberg algorithm. This package is really useful when the surface to optimize is non-strictly convex or far from a quadratic function. A new convergence criterion, the relative distance to maximum (RDM), allows the user to have a better confidence in the stopping points, other than basic algorithm stabilization.

VSURF

An R package for Variable Selection Using Random Forests. Available on CRAN, this package performs an automatic (meaning completely data-driven) variable selection procedure. Originally designed to deal with high dimensional data, it can also be applied to standard datasets.

R2GUESS

R2GUESS package is a wrapper of the GUESS (Graphical processing Unit Evolutionary Stochastic Search ) program. GUESS is a computationally optimised C++ implementation of a fully Bayesian variable selection approach that can analyse, in a genome-wide context, single and multiple responses in an integrated way. The program uses packages from the GNU Scientific Library (GSL) and offers the possibility to re-route computationally intensive linear algebra operations towards the Graphical Processing Unit (GPU) through the use of proprietary CULA-dense library.