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https://www.readbyqxmd.com/read/28420677/tcup-typing-and-characterization-of-bacteria-using-bottom-up-tandem-mass-spectrometry-proteomics
#1
Fredrik Boulund, Roger Karlsson, Lucia Gonzales-Siles, Anna Johnning, Nahid Karami, Omar Al-Bayati, Christina Ahren, Edward R B Moore, Erik Kristiansson
Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data is highly fragmented, making down-stream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS...
April 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#2
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28389638/imgmd-a-platform-for-the-integration-and-standardisation-of-in-silico-microbial-genome-scale-metabolic-models
#3
Chao Ye, Nan Xu, Chuan Dong, Yuannong Ye, Xuan Zou, Xiulai Chen, Fengbiao Guo, Liming Liu
Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28386247/gamola2-a-comprehensive-software-package-for-the-annotation-and-curation-of-draft-and-complete-microbial-genomes
#4
Eric Altermann, Jingli Lu, Alan McCulloch
Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28381997/reproducible-large-scale-neuroimaging-studies-with-the-openmole-workflow-management-system
#5
Jonathan Passerat-Palmbach, Romain Reuillon, Mathieu Leclaire, Antonios Makropoulos, Emma C Robinson, Sarah Parisot, Daniel Rueckert
OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28379466/mackinac-a-bridge-between-modelseed-and-cobrapy-to-generate-and-analyze-genome-scale-metabolic-models
#6
Michael Mundy, Helena Mendes-Soares, Nicholas Chia
Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms...
August 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28379299/fuento-functional-enrichment-for-bioinformatics
#7
David Weichselbaum, Bojan Zagrovic, Anton A Polyansky
Summary: The currently available functional enrichment software focuses mostly on gene expression analysis, whereby server- and graphical-user-interface-based tools with specific scope dominate the field. Here we present an efficient, user-friendly, multifunctional command-line-based functional enrichment tool ( fu-en-to ), tailored for the bioinformatics researcher. Availability and implementation: Source code and binaries freely available for download at github...
March 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369225/aozan-an-automated-post-sequencing-data-processing-pipeline
#8
Sandrine Perrin, Cyril Firmo, Sophie Lemoine, Stéphane Le Crom, Laurent Jourdren
Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion, and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports. Availability and Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www...
March 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334160/aqua-duct-a-ligands-tracking-tool
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
April 15, 2017: Bioinformatics
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