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UNLABELLED: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical...

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...

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel perfor-mance against the local interactive...

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously dev...

SUMMARY: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequen...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of th...

MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and ...

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version ...

An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation...

A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contra...

Materias / palabras clave: Bottleneck; Metagenomics; Computer science; Diamond; Sensitivity (control systems); Software; Search engine indexing; Speedup; Computational biology; Data mining; Bioinformatics; Parallel computing

Materias / palabras clave: Computer science; Flexibility (engineering); Dynamic programming; Software; Throughput; Index (typography); Sensitivity (control systems); Parallel computing; Algorithm; Computer hardware; Programming language; Operating...

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, r...

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified...

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 ...

Nowadays, the scientific applications are developed with more complexity and accuracy and these precisions need high computational resources to be executed. Also, the current trend in high performance computing (HPC) is ...

The Web has became an obiquitous resource for distributed computing making it relevant to investigate new ways of providing efficient access to services available at dedicated sites. Efficiency is an ever-increasing dema...

When IBM's John Backus first developed the Fortran programming language, back in 1957, he certainly never dreamt that it would become a world-wide success and still be going strong many years later. Given the oft-repeate...

Anticancer cytotoxic agents go through a process by which their antitumor activity-on the basis of the amount of tumor shrinkage they could generate-has been investigated. In the late 1970s, the International Union Again...

Most information in science, engineering and business has been recorded in form of text. This information can be found online in the World-Wide-Web. One of the major tools to support information access are the search eng...

InfiniBand (IBA) technology was developed to address the performance issues associated with messages movement among Endnodes and computer I/O devices. However, InfiniBand is also widely deployed within high performance c...