ASaiM: A Galaxy-based framework to analyze microbiota data

Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable

Crack propagation using XFEM coupled withAdaptative Mesh Refinement

International audienceThe eXtended Finite Element Method (XFEM) has been used in Cast3m tosimulate static and dynamic problems of crack propagation in elastic-plastic materials. Inthe context of non-linear behaviour we used over-integrated elements [3]. Computationof incremental propagation implies an accurate description of physical quantities (stress,strains, internal variables ...) in a limited area around the crack front, specilly when localciteria and inelastic materials are concerned. Then apriori ignorance of the propagationpath, forces us to use a really fine mesh of enriched elements in a rather large zone.Consequently the cost of this method increases drasticly for engineer-sized problems.Thus we decided to develop an adaptative mesh refinement tool, to create a finemeshed zone that will follow the crack front during the propagation, as illustrated on thefigure below. This tool is completed whith the XFEM method and limits the calculationtime with the number of small enriched elements.The procedure used to simulate a crack propagation with the XFEM method coupledwith an AMR tool in Cast3m, will be described. More particularly the presentation focuseson two important steps of this procedure 1) the refinement algorithm for enriched elements.2) the method used to transfer the mechanical fields from one mesh to another betweentwo steps of propagation, and the good properties of this field transfer.The efficency of the method is illustrated by an application case of crack propagationin elastic-plastic media in 3D

A local/global non-intrusive coupling approach for localized crack growth simulation

International audienceThe question of the inclusion of a crack and its propagation in a finite element (FE) model initially not intended for this, is a question which is still today the subject of numerous studies. A special effort is dedicated to the development of tools increasingly generic, flexible and simple to implement and to use. In this sense, X-FEM has achieved a first step towards clearly less intrusive simulation of fracture problems. To reduce further this intrusiveness, a new family of non-intrusive coupling algorithms has recently been intiated by [1]. Theses methods are dedicated to global FE model solved by a blackbox software in which a local phenomena (plasticity (1] or localized loading [2]) appears, that the global model is not able to account for. The idea is to develop a local/global coupling algorithm while avoiding any modification of the industrial code used to simulate the global problem. These coupling algorithms have been originally based on domain decomposition (DD) solvers [1,2]. Here an alternative algorithm based on a localised multigrid algorithm [3] is proposed for the simulation of mixed-mode crack propagation, while respecting the constraint of non-intrusiveness of the global problem [4]. For the global model, the contribution of the local patch consists in additional nodal efforts near the crack, which makes it compatible with most softwares. The shape of the local model is also adapted automatically during mixed mode propagatio