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https://www.readbyqxmd.com/read/29464735/molup-a-vmd-plugin-to-handle-qm-and-oniom-calculations-using-the-gaussian-software
#1
Henrique S Fernandes, Maria J Ramos, Nuno M F S A Cerqueira
The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations...
February 21, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29444236/findgse-estimating-genome-size-variation-within-human-and-arabidopsis-using-k-mer-frequencies
#2
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444234/threadna-predicting-dna-mechanics-contribution-to-sequence-selectivity-of-proteins-along-whole-genomes
#3
Jasmin Cevost, Cédric Vaillant, Sam Meyer, Burkhard Rost
Motivation: Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA's response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein-DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29425634/quantifying-medical-student-clinical-experiences-via-an-icd-code-logging-app
#4
Fred Rawlins, Cameron Sumpter, Dean Sutphin, Harold R Garner
OBJECTIVES: The logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students' clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status. MATERIALS AND METHODS: We have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers...
March 2018: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29419817/investigation-of-the-spatial-structure-and-interactions-of-the-genome-at-sub-kilobase-pair-resolution-using-t2c
#5
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
https://www.readbyqxmd.com/read/29413840/alphacal-a-new-user-friendly-tool-for-the-calibration-of-alpha-particle-sources
#6
A Fernández Timón, M Jurado Vargas, P Álvarez Gallardo, J Sánchez-Oro, L Peralta
In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources...
February 1, 2018: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29411163/mordred-a-molecular-descriptor-calculator
#7
Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita, Tatsuya Takagi
Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. To address these issues, we propose Mordred, a developed descriptor-calculation software application that can calculate more than 1800 two- and three-dimensional descriptors...
February 6, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29396867/the-gnat-a-new-tool-for-processing-nmr-data
#8
Laura Castañar, Guilherme Dal Poggetto, Adam Colbourne, Gareth A Morris, Mathias Nilsson
The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualizing and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g. Fourier transformation, baseline correction, phasing) is catered for within the programme, as well as more advanced techniques (e.g. reference deconvolution, pure shift FID reconstruction)...
February 2, 2018: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/29360956/primer3_masker-integrating-masking-of-template-sequence-with-primer-design-software
#9
Triinu Kõressaar, Maarja Lepamets, Lauris Kaplinski, Kairi Raime, Reidar Andreson, Maido Remm
Summary: Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3...
January 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342241/ipat-intelligent-prediction-and-association-tool-for-genomic-research
#10
Chunpeng James Chen, Zhiwu Zhang
Summary: The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340599/a-benchmark-study-of-scoring-methods-for-non-coding-mutations
#11
Damien Drubay, Daniel Gautheret, Stefan Michiels
Motivation: Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance. Results: We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases)...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29330118/using-the-ribodeblur-pipeline-to-recover-a-sites-from-yeast-ribosome-profiling-data
#12
Hao Wang, Carl Kingsford, C Joel McManus
Ribosome profiling has emerged as a powerful technique to study mRNA translation. Ribosome profiling has the potential to determine the relative quantities and locations of ribosomes on mRNA genome wide. Taking full advantage of this approach requires accurate measurement of ribosome locations. However, experimental inconsistencies often obscure the positional information encoded in ribosome profiling data. Here, we describe the Ribodeblur pipeline, a computational analysis tool that uses a maximum likelihood framework to infer ribosome positions from heterogeneous datasets...
January 9, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29300845/chronqc-a-quality-control-monitoring-system-for-clinical-next-generation-sequencing
#13
Nilesh R Tawari, Justine Jia Wen Seow, Perumal Dharuman, Jack L Ow, Shimin Ang, Arun George Devasia, Pauline C Ng
Summary: ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds, and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping...
December 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29240889/geoboost-accelerating-research-involving-the-geospatial-metadata-of-virus-genbank-records
#14
Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch, Graciela Gonzalez-Hernandez
Summary: GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates, and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH...
December 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29236969/damirseq-an-r-bioconductor-package-for-data-mining-of-rna-seq-data-normalization-feature-selection-and-classification
#15
Mattia Chiesa, Gualtiero I Colombo, Luca Piacentini
Summary: RNA-Seq is becoming the technique of choice for high-throughput transcriptome profiling, which, besides class comparison for differential expression, promises to be an effective and powerful tool for biomarker discovery. However, a systematic analysis of high-dimensional genomic data is a demanding task for such a purpose. DaMiRseq offers an organized, flexible and convenient framework to remove noise and bias, select the most informative features and perform accurate classification...
December 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29220101/report-of-aapm-task-group-162-software-for-planar-image-quality-metrology
#16
Ehsan Samei, Lynda C Ikejimba, Brian P Harrawood, John Rong, Ian A Cunningham, Michael J Flynn
PURPOSE: The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. METHODS: The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE)...
December 8, 2017: Medical Physics
https://www.readbyqxmd.com/read/29211825/bicycle-a-bioinformatics-pipeline-to-analyze-bisulfite-sequencing-data
#17
Osvaldo Graña, Hugo López-Fernández, Florentino Fdez-Riverola, David González Pisano, Daniel Glez-Peña
Summary: High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data...
December 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29187143/dmrfinder-efficiently-identifying-differentially-methylated-regions-from-methylc-seq-data
#18
John M Gaspar, Ronald P Hart
BACKGROUND: DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements...
November 29, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29186339/bioalcidae-samjs-and-vcffilterjs-object-oriented-formatters-and-filters-for-bioinformatics-files
#19
Pierre Lindenbaum, Richard Redon
Motivation: Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. Results: In this context, we wrote a set of tools named bioalcidae, samjs and vcffilterjs that reformat or filter files using a javascript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk)...
November 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29135934/ultrapse-a-universal-and-extensible-software-platform-for-representing-biological-sequences
#20
Pu-Feng Du, Wei Zhao, Yang-Yang Miao, Le-Yi Wei, Likun Wang
With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes...
November 14, 2017: International Journal of Molecular Sciences
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