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Abstract Metal-Organic Frameworks (MOFs) have attracted widespread attention for their applications in water-related contexts. A comprehensive understanding of the molecular-level interactions between water and MOFs is c...

The Global Flood Awareness System (GloFAS) is a promising flood-modelling tool available for most river basins worldwide. However, it contains inherent biases, notably linked to its spatial resolution. This study propose...

BACKGROUND: Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling...

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...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for informatio...

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related are...

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...

BACKGROUND: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reporte...

Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build struct...

CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-g...

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

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 ...

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU ...

MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis i...

The main objective of this paper centers on reviewing the evolution of Decision Support System´s (DSS) architectures, particularly as they apply to natural resources. Today it is difficult to conceive the existence of a...

El universo de estructuras químicas teóricas sintéticamente accesibles se calcula actualmente en 10100 compuestos. La Química Medicinal y la Industria Farmacéutica internacional en particular, ante la necesidad de a...

Agents repesent a new paradigm for developing software applications. In spite of the interest of this particular way of looking at problems, there is considerable discrepancy on exactly what is an agent and which are the...

Modern computers present a big gap between peak performance and sustained performance. There are many reasons for this situation, but mainly involving an inefficient usage of computational resources. Nowadays the memory ...

Segmentation is often a critical step in image analysis. Microscope image components show great variability of shapes, sizes, intensities and textures. An inaccurate segmentation conditions the ulterior quantification a...

"The statistical properties of Synthetic Aperture Radar (SAR) image texture reveal useful target characteristics. It is well-known that these images are affected by speckle and prone to extreme values due to double bounc...

(NOTE: Each chapter begins with an Introduction, and concludes with Exercises and References.) I. GETTING STARTED. 1. Aspects of Multivariate Analysis. Applications of Multivariate Techniques. The Organization of Data. D...

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of spec...

Variable selection is fundamental to high-dimensional statistical modeling, including nonparametric regression. Many approaches in use are stepwise selection procedures, which can be computationally expensive and ignore ...