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https://www.readbyqxmd.com/read/28334160/aqua-duct-a-ligands-tracking-tool
#1
Tomasz Magdziarz, Karolina Mitusinska, Sandra Goldowska, Alicja Pluciennik, Michal Stolarczyk, Magdalena Lugowska, Artur Góra
Motivation: The identification and tracking of molecules which enter active site cavity requires screening the positions of thousands of single molecules along several thousand molecular dynamic steps. To fill the existing gap between tools searching for tunnels and pathways and advanced tools employed for accelerated water flux investigations, we have developed AQUA-DUCT. Results: AQUA-DUCT is an easy-to-use tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28321440/neuronify-an-educational-simulator-for-neural-circuits
#2
Svenn-Arne Dragly, Milad Hobbi Mobarhan, Andreas Våvang Solbrå, Simen Tennøe, Anders Hafreager, Anders Malthe-Sørenssen, Marianne Fyhn, Torkel Hafting, Gaute T Einevoll
Educational software (apps) can improve science education by providing an interactive way of learning about complicated topics that are hard to explain with text and static illustrations. However, few educational apps are available for simulation of neural networks. Here, we describe an educational app, Neuronify, allowing the user to easily create and explore neural networks in a plug-and-play simulation environment. The user can pick network elements with adjustable parameters from a menu, i.e., synaptically connected neurons modelled as integrate-and-fire neurons and various stimulators (current sources, spike generators, visual, and touch) and recording devices (voltmeter, spike detector, and loudspeaker)...
March 2017: ENeuro
https://www.readbyqxmd.com/read/28315995/ligand-based-virtual-screening-under-partial-shape-constraints
#3
Mathias M von Behren, Matthias Rarey
Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure...
March 18, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28295580/specpad-device-independent-nmr-data-visualization-and-processing-based-on-the-novel-dart-programming-language-and-html5-web-technology
#4
Bruno Guigas
SpecPad is a new device-independent software program for the visualization and processing of one- and two-dimensional NMR time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks...
March 12, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28291762/the-xchemexplorer-graphical-workflow-tool-for-routine-or-large-scale-protein-ligand-structure-determination
#5
Tobias Krojer, Romain Talon, Nicholas Pearce, Patrick Collins, Alice Douangamath, Jose Brandao-Neto, Alexandre Dias, Brian Marsden, Frank von Delft
XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28253237/translation-complex-profile-sequencing-to-study-the-in-vivo-dynamics-of-mrna-ribosome-interactions-during-translation-initiation-elongation-and-termination
#6
Nikolay E Shirokikh, Stuart K Archer, Traude H Beilharz, David Powell, Thomas Preiss
Messenger RNA (mRNA) translation is a tightly controlled process that is integral to gene expression. It features intricate and dynamic interactions of the small and large subunits of the ribosome with mRNAs, aided by multiple auxiliary factors during distinct initiation, elongation and termination phases. The recently developed ribosome profiling method can generate transcriptome-wide surveys of translation and its regulation. Ribosome profiling records the footprints of fully assembled ribosomes along mRNAs and thus primarily interrogates the elongation phase of translation...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28211003/an-easy-to-build-low-budget-point-of-care-ultrasound-simulator-from-linux-to-a-web-based-solution
#7
Domagoj Damjanovic, Ulrich Goebel, Benedikt Fischer, Martin Huth, Hartmut Breger, Hartmut Buerkle, Axel Schmutz
BACKGROUND: Hands-on training in point-of-care ultrasound (POC-US) should ideally comprise bedside teaching, as well as simulated clinical scenarios. High-fidelity phantoms and portable ultrasound simulation systems are commercially available, however, at considerable costs. This limits their suitability for medical schools. A Linux-based software for Emergency Department Ultrasound Simulation (edus2TM) was developed by Kulyk and Olszynski in 2011. Its feasibility for POC-US education has been well-documented, and shows good acceptance...
December 2017: Critical Ultrasound Journal
https://www.readbyqxmd.com/read/28155723/locexpress-a-web-server-for-efficiently-estimating-expression-of-novel-transcripts
#8
Mei Hou, Feng Tian, Shuai Jiang, Lei Kong, Dechang Yang, Ge Gao
BACKGROUND: The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. RESULTS: Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines)...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28130233/a-comprehensive-quality-control-workflow-for-paired-tumor-normal-ngs-experiments
#9
Christopher M Schroeder, Franz J Hilke, Markus W Löffler, Michael Bitzer, Florian Lenz, Marc Sturm
Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additionally metrics specific for tumor-normal pairs can be calculated...
January 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108450/netland-quantitative-modeling-and-visualization-of-waddington-s-epigenetic-landscape-using-probabilistic-potential
#10
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
Waddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks. Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington's landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of gene regulatory networks (GRNs), and visualizing the corresponding Waddington's epigenetic landscape in three dimensions without restriction on the number of genes in a GRN...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28104627/mappi-dat-data-management-and-analysis-for-protein-protein-interaction-data-from-the-high-throughput-mappit-cell-microarray-platform
#11
Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens
Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge...
January 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#12
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#13
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28076851/pse-analysis-a-python-package-for-dna-rna-and-protein-peptide-sequence-analysis-based-on-pseudo-components-and-kernel-methods
#14
Bin Liu, Hao Wu, Deyuan Zhang, Xiaolong Wang, Kuo-Chen Chou
To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28069593/knime4ngs-a-comprehensive-toolbox-for-next
#15
Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, Michael Kluge, Kaarin Ahomaa, Marie-Sophie Friedl, Sebastian J Kopetzky, Jan-Dominik Quell, H- Werner Mewes, Robert Küffner
Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis...
January 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28064377/octopus-a-platform-for-the-virtual-high-throughput-screening-of-a-pool-of-compounds-against-a-set-of-molecular-targets
#16
Eduardo Habib Bechelane Maia, Vinícius Alves Campos, Bianca Dos Reis Santos, Marina Santos Costa, Iann Gabriel Lima, Sandro J Greco, Rosy I M A Ribeiro, Felipe M Munayer, Alisson Marques da Silva, Alex Gutterres Taranto
Octopus is an automated workflow management tool that is scalable for virtual high-throughput screening (vHTS). It integrates MOPAC2016, MGLTools, PyMOL, and AutoDock Vina. In contrast to other platforms, Octopus can perform docking simulations of an unlimited number of compounds into a set of molecular targets. After generating the ligands in a drawing package in the Protein Data Bank (PDB) format, Octopus can carry out geometry refinement using the semi-empirical method PM7 implemented in MOPAC2016. Docking simulations can be performed using AutoDock Vina and can utilize the Our Own Molecular Targets (OOMT) databank...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28062442/sine_scan-an-efficient-tool-to-discover-short-interspersed-nuclear-elements-sines-in-large-scale-genomic-datasets
#17
Hongliang Mao, Hao Wang
MOTIVATION: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. RESULTS: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element...
January 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28043542/the-analysis-of-exosomal-micro-rnas-in-peripheral-blood-mononuclear-cell-derived-macrophages-after-infection-with-bacillus-calmette-gu%C3%A3-rin-by-rna-sequencing
#18
Esmaeil Mortaz, Shamila D Alipoor, Payam Tabarsi, Ian M Adcock, Johan Garssen, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Tuberculosis (TB) is a major global threat to human health, especially in low-income countries. The diagnosis of TB is challenging because of the limitations of specificity and sensitivity with the current diagnostics. Novel, selective biomarkers for TB would be of great practical value. Exosomes are bioactive vesicles with 30-100nm in diameter, which are secreted from almost all cell types and are found in virtually every human body fluid. Exosomes transport micro-RNAs (miRNAs), which are post-transcriptional regulators of gene expression, around the body and allow miRNAs to modulate biological pathways in target cells...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28028736/fast-h-drop-a-thirty-times-accelerated-version-of-h-drop-for-interactive-svm-based-prediction-of-helical-domain-linkers
#19
Tambi Richa, Soichiro Ide, Ryosuke Suzuki, Teppei Ebina, Yutaka Kuroda
Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol...
December 27, 2016: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28013191/partitionfinder-2-new-methods-for-selecting-partitioned-models-of-evolution-for-molecular-and-morphological-phylogenetic-analyses
#20
Robert Lanfear, Paul B Frandsen, April M Wright, Tereza Senfeld, Brett Calcott
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems...
December 23, 2016: Molecular Biology and Evolution
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