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The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and wide...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have con...

Materias / palabras clave: Turbulence; Turbulence kinetic energy; Computation; K-epsilon turbulence model; K-omega turbulence model; Dissipation; Mechanics; Flow (mathematics); Statistical physics; Turbulence modeling; Range (aeronautics); Physics

"This work describes the use of entomological studies combined with in silico models (computer simulations derived from numerical models) to assess the efficacy of a novel device for controlled release of spatial repel...

"The steel industry faces increasing challenges in managing product diversity, maintaining competitiveness, and improving operational efficiency. Within this context, recommendation systems present a promising opportunit...

Three alternatives within the method of assignment by classes are presented for the calculation of individuals lifetime in genetic algorithms with varying population size. (GAVaPS). In the proposed strategy (assignment b...

Globally optimal triangulations are difficult to be found by deterministic methods as, for most type of criteria, no polynomial algorithm is known. In this work, we consider the Minimum Weight Triangulation (MWT) problem...

SIR 97 is the integration of two programs, SIR 92 and CAOS , the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new feature...

The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crysta...

The resolution of optimization problems is of great interest nowadays and has encouraged the development of various information technology methods to attempt solving them. There are several problems related to Software E...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological inte...

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a st...

We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection me...

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we intro...

Machine learning addresses the question of how to build computers that improve automatically through experience. It is one of today's most rapidly growing technical fields, lying at the intersection of computer science a...

A basic problem in computer vision is to understand the structure of a real world scene given several images of it. Techniques for solving this problem are taken from projective geometry and photogrammetry. Here, the aut...

Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains ...

A new direct difference method for the computation of molecular interactions has been based on a bivariational transcorrelated treatment, together with special methods for the balancing of other errors. It appears that t...

BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...

Evolutionary algorithms (EAs) are often well-suited for optimization problems involving several, often conflicting objectives. Since 1985, various evolutionary approaches to multiobjective optimization have been develope...

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, i...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...