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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...

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redoc...

The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations func...

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...

New software, OLEX2 , has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical use...

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package...

Designing PCR and sequencing primers are essential activities for molecular biologists around the world. This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs. 1–4...

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

UNLABELLED: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software...

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...

Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign n...

To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development invol...

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete...

Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune ...

We propose a novel image denoising strategy based on an enhanced sparse representation in transform domain. The enhancement of the sparsity is achieved by grouping similar 2-D image fragments (e.g., blocks) into 3-D data...

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures be...

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...

Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrich...

In this paper we are concerned with the practical issues of working with data sets common to finance, statistics, and other related fields. pandas is a new library which aims to facilitate working with these data sets an...

Materias / palabras clave: Range (aeronautics); Software; Set (abstract data type); Tracking (education); Computer science; Physics; Systems engineering; Computational science; Aerospace engineering; Programming language; Engineering; Pedagogy

Abstract Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming l...

Abstract We investigate the use of multiple transmitting and/or receiving antennas for single user communications over the additive Gaussian channel with and without fading. We derive formulas for the capacities and erro...

The way that information propagates in neural networks is of great importance. In this paper, we propose Path Aggregation Network (PANet) aiming at boosting information flow in proposal-based instance segmentation framew...

This paper presents a new vision Transformer, called Swin Transformer, that capably serves as a general-purpose backbone for computer vision. Challenges in adapting Transformer from language to vision arise from differen...