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https://www.readbyqxmd.com/read/28994627/mybrain-a-novel-eeg-embedded-system-for-epilepsy-monitoring
#1
Francisco Pinho, João Cerqueira, José Correia, Nuno Sousa, Nuno Dias
The World Health Organisation has pointed that a successful health care delivery, requires effective medical devices as tools for prevention, diagnosis, treatment and rehabilitation. Several studies have concluded that longer monitoring periods and outpatient settings might increase diagnosis accuracy and success rate of treatment selection. The long-term monitoring of epileptic patients through electroencephalography (EEG) has been considered a powerful tool to improve the diagnosis, disease classification, and treatment of patients with such condition...
October 10, 2017: Journal of Medical Engineering & Technology
https://www.readbyqxmd.com/read/28992259/wgssat-a-high-throughput-computational-pipeline-for-mining-and-annotation-of-ssr-markers-from-whole-genomes
#2
Manmohan Pandey, Ravindra Kumar, Prachi Srivastava, Suyash Agarwal, Shreya Srivastava, N S Nagpure, J K Jena, Basdeo Kushwaha
Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers...
September 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28981423/premer-a-tool-to-infer-biological-networks
#3
Alejandro F Villaverde, Kolja Becker, Julio R Banga
Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems...
October 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28980073/ligro-a-graphical-user-interface-for-protein-ligand-molecular-dynamics
#4
Luciano Porto Kagami, Gustavo Machado das Neves, Alan Wilter Sousa da Silva, Rafael Andrade Caceres, Daniel Fábio Kawano, Vera Lucia Eifler-Lima
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration)...
October 4, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28968872/pyscestoolbox-a-collection-of-metabolic-pathway-analysis-tools
#5
Carl D Christensen, Jan-Hendrik S Hofmeyr, Johann M Rohwer
Summary: PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalised supply-demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects of enzyme-catalysed reactions. Each tool addresses a different aspect of metabolic behaviour, control, and regulation; the tools complement each other and can be used in conjunction to better understand higher-level system behaviour...
September 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28968637/dugong-a-docker-image-based-on-ubuntu-linux-focused-on-reproducibility-and-replicability-for-bioinformatics-analyses
#6
Fabiano B Menegidio, Daniela L Jabes, Regina Costa de Oliveira, Luiz R Nunes
Summary: This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects...
September 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28961771/cloud-based-interactive-analytics-for-terabytes-of-genomic-variants-data
#7
Cuiping Pan, Gregory McInnes, Nicole Deflaux, Michael Snyder, Jonathan Bingham, Somalee Datta, Philip S Tsao
Motivation: Large scale genomic sequencing is now widely used to decipher questions in diverse realms such as biological function, human diseases, evolution, ecosystems, and agriculture. With the quantity and diversity these data harbor, a robust and scalable data handling and analysis solution is desired. Results: We present interactive analytics using a cloud-based columnar database built on Dremel to perform information compression, comprehensive quality controls, and biological information retrieval in large volumes of genomic data...
July 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28961742/bsviewer-a-genotype-preserving-nucleotide-level-visualizer-for-bisulfite-sequencing-data
#8
Kun Sun, Fiona F M Lun, Peiyong Jiang, Hao Sun
Motivation: The bisulfite sequencing technology has been widely used to study the DNA methylation profile in many species. However, most of the current visualization tools for bisulfite sequencing data only provide high-level views (i.e., overall methylation densities) while miss the methylation dynamics at nucleotide level. Meanwhile, they also focus on CpG sites while omit other information (such as genotypes on SNP sites) which could be helpful for interpreting the methylation pattern of the sequencing data...
August 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28936668/rna-seq-data-analysis-protocol-combining-in-house-and-publicly-available-data
#9
Marc W Schmid
Comparing gene expression profiles measured in a wide range of different tissue types, at different developmental stages, or under different environmental conditions can yield valuable insights into the mechanisms of cell/tissue specification and differentiation, or identify cell/tissue-type specific responses to environmental stimuli. Critical for such comparisons is the identical processing of data from different sources. This may also include the integration of a novel data set into an existing collection of data sets (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28917015/metronome-lkm-an-open-source-virtual-keyboard-driver-to-measure-experiment-software-latencies
#10
Pablo Garaizar, Miguel A Vadillo
Experiment software is often used to measure reaction times gathered with keyboards or other input devices. In previous studies, the accuracy and precision of time stamps has been assessed through several means: (a) generating accurate square wave signals from an external device connected to the parallel port of the computer running the experiment software, (b) triggering the typematic repeat feature of some keyboards to get an evenly separated series of keypress events, or (c) using a solenoid handled by a microcontroller to press the input device (keyboard, mouse button, touch screen) that will be used in the experimental setup...
September 15, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28805044/nm%C3%AF-improved-re-implementation-of-nm-a-software-for-estimating-gene-dispersal-and-mating-patterns
#11
Igor J Chybicki
This paper introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multi-core processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighborhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system...
August 14, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28803247/potential-gender-related-aging-processes-occur-earlier-and-faster-in-the-vermis-of-patients-with-bipolar-disorder-an-mri-study
#12
Marta Serati, Giuseppe Delvecchio, Giulia Orsenigo, Cinzia Perlini, Marco Barillari, Mirella Ruggeri, Alfredo Carlo Altamura, Marcella Bellani, Paolo Brambilla
BACKGROUND: In the last decades, there has been increasing interest in investigating the role of the vermis in bipolar disorder (BD), especially because of its involvement in cognitive processes. The main aims of this study were to explore the integrity of the vermis and elucidate the role of demographic and clinical variables on vermis volumes in BD patients, stratified according to gender. METHODS: T1-weighted images were obtained for 38 BD patients and 38 healthy controls using a 1...
August 12, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/28780378/homblocks-a-multiple-alignment-construction-pipeline-for-organelle-phylogenomics-based-on-locally-collinear-block-searching
#13
Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multi-gene alignments. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multi-gene alignment in a few hours...
August 2, 2017: Genomics
https://www.readbyqxmd.com/read/28780100/technical-note-pagell-v-1-5-a-flexible-parametric-program-for-the-bayesian-analysis-of-longevity-data-within-the-context-of-animal-breeding
#14
J Casellas, L C Brito
This technical note presents the program PaGELL v.1.5 (Parametric Genetic Evaluation of Lifespan in Livestock), a flexible software program to analyze (right-censored) longevity data in livestock populations, with a special emphasis on the genetic evaluation of the breeding stock. This software relies on a parametric generalization of the proportional hazard model; more specifically, the baseline hazard function follows a Weibull process and flexibility is gained by including an additional time-dependent effect with the number of change points defined by the user...
August 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28733406/genetic-interaction-score-s-score-calculation-clustering-and-visualization-of-genetic-interaction-profiles-for-yeast
#15
Assen Roguev, Colm J Ryan, Jiewei Xu, Isabelle Colson, Edgar Hartsuiker, Nevan Krogan
This protocol describes computational analysis of genetic interaction screens, ranging from data capture (plate imaging) to downstream analyses. Plate imaging approaches using both digital camera and office flatbed scanners are included, along with a protocol for the extraction of colony size measurements from the resulting images. A commonly used genetic interaction scoring method, calculation of the S-score, is discussed. These methods require minimal computer skills, but some familiarity with MATLAB and Linux/Unix is a plus...
July 21, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28710774/ucsf-chimerax-meeting-modern-challenges-in-visualization-and-analysis
#16
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin
UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This paper highlights some specific advances in the areas of visualization and usability, performance, and extensibility...
July 14, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28699123/the-tool-for-the-automatic-analysis-of-lexical-sophistication-taales-version-2-0
#17
Kristopher Kyle, Scott Crossley, Cynthia Berger
This study introduces the second release of the Tool for the Automatic Analysis of Lexical Sophistication (TAALES 2.0), a freely available and easy-to-use text analysis tool. TAALES 2.0 is housed on a user's hard drive (allowing for secure data processing) and is available on most operating systems (Windows, Mac, and Linux). TAALES 2.0 adds 316 indices to the original tool. These indices are related to word frequency, word range, n-gram frequency, n-gram range, n-gram strength of association, contextual distinctiveness, word recognition norms, semantic network, and word neighbors...
July 11, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28693417/ace-an-efficient-and-sensitive-tool-to-detect-insecticide-resistance-associated-mutations-in-insect-acetylcholinesterase-from-rna-seq-data
#18
Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu, Fei Li
BACKGROUND: Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been widely used in this field, they are time-consuming and inefficient, and typically have a high false positive rate. Acetylcholinesterases (Ace) is the neural target of the widely used organophosphate (OP) and carbamate insecticides. However, there is not any software available to detect insecticide resistance associated mutations in RNA-Seq data at present...
July 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28676075/sgnesr-an-r-package-for-simulating-gene-expression-data-from-an-underlying-real-gene-network-structure-considering-delay-parameters
#19
Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
BACKGROUND: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles...
July 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28666314/gpu-powered-model-analysis-with-pysb-cupsoda
#20
Leonard A Harris, Marco S Nobile, James C Pino, Alexander L R Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F Lopez
Summary: A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework...
June 28, 2017: Bioinformatics
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