Search results for "Computation"

Lightweight LCP construction for next-generation sequencing datasets

2012

The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection would facilitate the rapid computation of maximal exact matches, shortest unique substrings and shortest absent words. CPU-efficient algorithms for computing the LCP of a string have been described in the literature, but require the presence in RAM of large data structures. This prevents such methods from being feasible for NGS datasets. In this paper we propose the first lightweight method that simultaneously computes, via sequential scans, the LCP and B…

Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software

2020

Next-generation sequencing (NGS) is now widely used in microbiology to explore genome evolution and the structure of pathogen outbreaks. Bioinformatics pipelines readily detect single-nucleotide polymorphisms or short indels. However, bacterial genomes also evolve through the action of small transposable elements called insertion sequences (ISs), which are difficult to detect due to their short length and multiple repetitions throughout the genome. We designed panISa software for the ab initio detection of IS insertions in the genomes of prokaryotes. PanISa has been released as open source software (GPL3) available from https://github.com/bvalot/panISa. In this study, we assessed the utilit…

Genomic and Proteomic Analysis of Wine Yeasts

2011

Publisher Summary Saccharomyces cerevisiae is the main microorganism involved in wine fermentation. It has been used as a model organism in molecular biology for many years and is the only wine yeast species for which abundant genomic and proteomic information is available. Most of the techniques currently used in functional genomics and proteomics were initially developed in this yeast. The fact that S. cerevisiae was the first microorganism to be widely used in the development of genome technology allowed other phylogenetically related yeasts to be analyzed subsequently in global sequencing projects, and the use of comparative genomics has since led to important conclusions regarding gene…

Games and Bisimulations for Intuitionistic First-Order Kripke Models

2021

The aim of this paper is to introduce the notion of a game for intuitionisticfirst-order Kripke models. We also establish links between notions presented here and thenotions of logical equivalence and bounded bisimulation for intuitionistic first-order Kripkemodels, and the Ehrenfeucht–Fra ̈ıss ́e game for classical first-order structures.

Richard von Mises’ work for ZAMM until his emigration in 1933 and glimpses of the later history of ZAMM

2020

Correlation analysis of the power law parameters for viscosity of some engineering fluids

2017

Knowledge and estimation of transport properties of fluids which are sensitive to temperature variation like viscosity are necessary in mass flow and heat transfer computation. In the present work,...

Multi-Resolution error analysis of predicted absorption coefficients. Method and application to the infrared spectrum of methane at high temperature.

2010

La version V2 inclut les modifications proposées par les reviewers.; International audience; A general method for the estimation of the confidence interval of molecular absorption coefficients is presented. Statistical numerical experiments are implemented to quantify the propagation of errors from line parameters to absorption coefficients or cross-sections as a function of the resolution. The method uses line parameter predictions (position and intensity) with estimated uncertainties derived from global polyad models. This work is especially intended to provide expert information for applications requiring theoretical predictions for which the present state of the art of line by line high…

Towards Stable Radial Basis Function Methods for Linear Advection Problems

2021

In this work, we investigate (energy) stability of global radial basis function (RBF) methods for linear advection problems. Classically, boundary conditions (BC) are enforced strongly in RBF methods. By now it is well-known that this can lead to stability problems, however. Here, we follow a different path and propose two novel RBF approaches which are based on a weak enforcement of BCs. By using the concept of flux reconstruction and simultaneous approximation terms (SATs), respectively, we are able to prove that both new RBF schemes are strongly (energy) stable. Numerical results in one and two spatial dimensions for both scalar equations and systems are presented, supporting our theoret…

An atlas- and data-driven approach to initializing reaction-diffusion systems in computer cardiac electrophysiology

2016

The cardiac electrophysiology (EP) problem is governed by a nonlinear anisotropic reaction-diffusion system with a very rapidly varying reaction term associated with the transmembrane cell current. The nonlinearity associated with the cell models requires a stabilization process before any simulation is performed. More importantly, when used in a 3-dimensional (3D) anatomy, it is not sufficient to perform this stabilization on the basis of isolated cells only, since the coupling of the different cells through the tissue greatly modulates the dynamics of the system. Therefore, stabilization of the system must be performed on the entire 3D model. This work develops a novel procedure for the i…

Membrane Deformation and Its Effects on Flow and Mass Transfer in the Electromembrane Processes

2019

In the membrane processes, a trans-membrane pressure (TMP) may arise due to design features or operating conditions. In most applications, stacks for electrodialysis (ED) or reverse electrodialysis (RED) operate at low TMP (&lt