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Natural language understanding systems require a knowledge base provided with formal representations reflecting the structure of human beings' cognitive system. Although surface semantics can be sufficient in some other ...

A common feature in biological neuromuscular systems is the redundancy in joint actuation. Understanding how these redundancies are resolved in typical joint movements has been a long-standing problem in biomechanics, ne...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

BACKGROUND: Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely us...

VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3 , implementing new features including drawing the exte...

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...

Subjects / keywords: Program structure; Data structure; Downstream (manufacturing); Computer science; Data mining; Biology; Computational science; Programming language; Engineering; Operations management

In the Python world, NumPy arrays are the standard representation for numerical data and enable efficient implementation of numerical computations in a high-level language. As this effort shows, NumPy performance can be ...

Subjects / keywords: Text processing (Computer science); Genetic algorithms; Computational linguistics

MOTIVATION: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end librarie...

Subjects / keywords: Genomics; Computational biology; Profiling (computer programming); Human genome; Genome; Exome sequencing; Biology; Exome; Visualization; Genome browser; Data science; Computer science

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, an...

We introduce and discuss a new computational model for the HermiteLagrange interpolation with nonlinear classes of polynomial interpolants. We distinguish between an interpolation problem and an algorithm that solves it....

Virtualization has been on the increase of attention through the past few years. It enables the execution of many independent operational systems on an only operational system. It makes feasible a simulation of an interc...

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been...

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

Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it ...