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https://www.readbyqxmd.com/read/28710774/ucsf-chimerax-meeting-modern-challenges-in-visualization-and-analysis
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28582538/breakpoint-surveyor-a-pipeline-for-structural-variant-visualization
#6
Matthew A Wyczalkowski, Kristine M Wylie, Song Cao, Michael D McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C Wendl, Li Ding
Summary: BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-Seq expression into a single comprehensive figure. Availability: Source code and sample data freely available for download at https://github...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575169/md-task-a-software-suite-for-analyzing-molecular-dynamics-trajectories
#7
David K Brown, David L Penkler, Olivier Sheik Amamuddy, Caroline Ross, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop
Summary: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28540779/planning-optimisation-and-evaluation-of-hyperthermia-treatments
#8
H P Kok, A N T J Kotte, J Crezee
BACKGROUND: Hyperthermia treatment planning using dedicated simulations of power and temperature distributions is very useful to assist in hyperthermia applications. This paper describes an advanced treatment planning software package for a wide variety of applications. METHODS: The in-house developed C++ software package Plan2Heat runs on a Linux operating system. Modules are available to perform electric field and temperature calculations for many heating techniques...
March 8, 2017: International Journal of Hyperthermia
https://www.readbyqxmd.com/read/28525968/survivalgwas_sv-software-for-the-analysis-of-genome-wide-association-studies-of-imputed-genotypes-with-time-to-event-outcomes
#9
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Analysis of genome-wide association studies (GWAS) with "time to event" outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, disease remission or the occurrence of an adverse drug reaction. However, methodology and software that can efficiently handle the scale and complexity of genetic data from GWAS with time to event outcomes has not been extensively developed. RESULTS: SurvivalGWAS_SV is an easy to use software implemented using C# and run on Linux, Mac OS X & Windows operating systems...
May 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28503844/typeloader-a-fast-and-efficient-automated-workflow-for-the-annotation-and-submission-of-novel-full-length-hla-alleles
#10
V Surendranath, V Albrecht, J D Hayhurst, B Schöne, J Robinson, S G E Marsh, A H Schmidt, V Lange
Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database...
July 2017: HLA
https://www.readbyqxmd.com/read/28503667/neopeptide-analyser-a-software-tool-for-neopeptide-discovery-in-proteomics-data
#11
Mandy Peffers, Andrew R Jones, Antony McCabe, James Anderson
Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called 'neopeptides', i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the in vitro use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow...
April 7, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28486579/biomake-a-gnu-make-compatible-utility-for-declarative-workflow-management
#12
Ian H Holmes, Christopher J Mungall
. The Unix "make" program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. . We present BioMake, a make-like utility that is compatible with most features ofGNUMake and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog...
May 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28481978/application-of-the-cghra-framework-to-the-genomic-characterization-of-diffuse-large-b-cell-lymphoma
#13
Sylvain Mareschal, Philippe Ruminy, Marion Alcantara, Céline Villenet, Martin Figeac, Sydney Dubois, Philippe Bertrand, Abdelilah Bouzelfen, Pierre-Julien Viailly, Dominique Penther, Hervé Tilly, Christian Bastard, Fabrice Jardin
Motivation: Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyse such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. Results: The cghRA framework combines a user-friendly graphical interface and a powerful objectoriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#14
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28480121/alchemy-a-web-2-0-real-time-quality-assurance-platform-for-human-immunodeficiency-virus-hepatitis-c-virus-and-bk-virus-quantitation-assays
#15
Emmanuel Agosto-Arroyo, Gina M Coshatt, Thomas S Winokur, Shuko Harada, Seung L Park
BACKGROUND: The molecular diagnostics laboratory faces the challenge of improving test turnaround time (TAT). Low and consistent TATs are of great clinical and regulatory importance, especially for molecular virology tests. Laboratory information systems (LISs) contain all the data elements necessary to do accurate quality assurance (QA) reporting of TAT and other measures, but these reports are in most cases still performed manually: a time-consuming and error-prone task. The aim of this study was to develop a web-based real-time QA platform that would automate QA reporting in the molecular diagnostics laboratory at our institution, and minimize the time expended in preparing these reports...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28476995/parallel-implementation-of-d-phylo-algorithm-for-maximum-likelihood-clusters
#16
Shamita Malik, Dolly Sharma, Sunil Kumar Khatri
This study explains a newly developed parallel algorithm for phylogenetic analysis of DNA sequences. The newly designed D-Phylo is a more advanced algorithm for phylogenetic analysis using maximum likelihood approach. The D-Phylo while misusing the seeking capacity of k-means keeps away from its real constraint of getting stuck at privately conserved motifs. The authors have tested the behaviour of D-Phylo on Amazon Linux Amazon Machine Image(Hardware Virtual Machine)i2.4xlarge, six central processing unit, 122 GiB memory, 8 × 800 Solid-state drive Elastic Block Store volume, high network performance up to 15 processors for several real-life datasets...
March 2017: IET Nanobiotechnology
https://www.readbyqxmd.com/read/28469375/numericware-i-identical-by-state-matrix-calculator
#17
REVIEW
Bongsong Kim, William D Beavis
We introduce software, Numericware i, to compute identical by state (IBS) matrix based on genotypic data. Calculating an IBS matrix with a large dataset requires large computer memory and takes lengthy processing time. Numericware i addresses these challenges with 2 algorithmic methods: multithreading and forward chopping. The multithreading allows computational routines to concurrently run on multiple central processing unit (CPU) processors. The forward chopping addresses memory limitation by dividing a dataset into appropriately sized subsets...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28464826/microtaboo-a-general-and-practical-solution-to-the-k-disjoint-problem
#18
Mohammed Al-Jaff, Eric Sandström, Manfred Grabherr
BACKGROUND: A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem...
May 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28464287/geno-diver-a-combined-coalescence-and-forward-in-time-simulator-for-populations-undergoing-selection-for-complex-traits
#19
J T Howard, F Tiezzi, J E Pryce, C Maltecca
Geno-Diver is a combined coalescence and forward-in-time simulator designed to simulate complex traits with a quantitative and/or fitness component and implement multiple selection and mating strategies utilizing pedigree or genomic information. The simulation is carried out in two steps. The first step generates whole-genome sequence data for founder individuals. A variety of trait architectures can be generated for quantitative and fitness traits along with their covariance. The second step generates new individuals forward-in-time based on a variety of selection and mating scenarios...
May 2, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28453688/edlib-a-c-c%C3%A2-library-for-fast-exact-sequence-alignment-using-edit-distance
#20
Martin Šošic, Mile Šikic
Summary: We present Edlib, an open-source C/C ++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be easily adopted as a building block for future bioinformatics tools. Availability and Implementation: Source code, installation instructions and test data are freely available for download at https://github...
May 1, 2017: Bioinformatics
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