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https://www.readbyqxmd.com/read/28724111/agricultural-conservation-planning-framework-3-land-use-and-field-boundary-database-development-and-structure
#1
Mark D Tomer, David E James, Claudette M J Sandoval-Green
Conservation planning information is important for identifying options for watershed water quality improvement and can be developed for use at field, farm, and watershed scales. Translation across scales is a key issue impeding progress at watershed scales because watershed improvement goals must be connected with implementation of farm- and field-level conservation practices to demonstrate success. This is particularly true when examining alternatives for "trap and treat" practices implemented at agricultural-field edges to control (or influence) water flows through fields, landscapes, and riparian corridors within agricultural watersheds...
May 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28723960/a-validation-of-11-body-condition-indices-in-a-giant-snake-species-that-exhibits-positive-allometry
#2
Bryan G Falk, Ray W Snow, Robert N Reed
Body condition is a gauge of the energy stores of an animal, and though it has important implications for fitness, survival, competition, and disease, it is difficult to measure directly. Instead, body condition is frequently estimated as a body condition index (BCI) using length and mass measurements. A desirable BCI should accurately reflect true body condition and be unbiased with respect to size (i.e., mean BCI estimates should not change across different length or mass ranges), and choosing the most-appropriate BCI is not straightforward...
2017: PloS One
https://www.readbyqxmd.com/read/28723908/sorting-cells-by-their-density
#3
Nazila Norouzi, Heran C Bhakta, William H Grover
Sorting cells by their type is an important capability in biological research and medical diagnostics. However, most cell sorting techniques rely on labels or tags, which may have limited availability and specificity. Sorting different cell types by their different physical properties is an attractive alternative to labels because all cells intrinsically have these physical properties. But some physical properties, like cell size, vary significantly from cell to cell within a cell type; this makes it difficult to identify and sort cells based on their sizes alone...
2017: PloS One
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#4
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28716000/quantiprot-a-python-package-for-quantitative-analysis-of-protein-sequences
#5
Bogumił M Konopka, Marta Marciniak, Witold Dyrka
BACKGROUND: The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. RESULTS: Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28715209/comparison-of-the-predictive-performance-and-interpretability-of-random-forest-and-linear-models-on-benchmark-datasets
#6
Richard Liam Marchese Robinson, Anna Palczewska, Jan Palczewski, Nathan Kidley
The ability to interpret the predictions made by quantitative structure activity relationships (QSARs) offers a number of advantages. Whilst QSARs built using non-linear modelling approaches, such as the popular Random Forest algorithm, might sometimes be more predictive than those built using linear modelling approaches, their predictions have been perceived as difficult to interpret. However, a growing number of approaches have been proposed for interpreting non-linear QSAR models in general and Random Forest in particular...
July 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28706482/samuroi-a-python-based-software-tool-for-visualization-and-analysis-of-dynamic-time-series-imaging-at-multiple-spatial-scales
#7
Martin Rueckl, Stephen C Lenzi, Laura Moreno-Velasquez, Daniel Parthier, Dietmar Schmitz, Sten Ruediger, Friedrich W Johenning
The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28696459/the-origin-of-the-debye-relaxation-in-liquid-water-and-fitting-the-high-frequency-excess-response
#8
Daniel C Elton
We critically review the literature on the Debye absorption peak of liquid water and the excess response found on the high frequency side of the Debye peak. We find a lack of agreement on the microscopic phenomena underlying both of these features. To better understand the molecular origin of Debye peak we ran large scale molecular dynamics simulations and performed several different distance-dependent decompositions of the low frequency dielectric spectra, finding that it involves processes that take place on scales of 1...
July 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28696409/a-global-multiproxy-database-for-temperature-reconstructions-of-the-common-era
#9
(no author information available yet)
Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial...
July 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28695272/cardiovascular-effects-of-histamine-in-three-widely-diverse-species-of-reptiles
#10
Nini Skovgaard, Augusto S Abe, Edwin W Taylor, Tobias Wang
The cardiovascular system of vertebrates is regulated by a vast number of regulatory factors, including histamine. In pythons, histamine induces a strong tachycardia and dilates the systemic vasculature, which resembles the cardiovascular response to the elevated metabolic rate during digestion. In fact, there is an important role of increased histaminergic tone on the heart during the initial 24 h of digestion in pythons. Whilst the cardiovascular effects of histamine are well studied in pythons, little is known about the effects in other groups of reptiles...
July 10, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28692267/is-multitask-deep-learning-practical-for-pharma
#11
Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P Sheridan, Vijay S Pande
Multitask deep learning has emerged as a powerful tool for computational drug discovery. However, despite a number of preliminary studies, multitask deep networks have yet to be widely deployed in the pharmaceutical and biotech industries. This lack of acceptance stems from both software difficulties and from lack of understanding of the robustness of multitask deep networks. Our work aims to resolve both of these barriers to adoption. We introduce a high-quality open-source implementation of multitask deep networks as part of the DeepChem open-source platform...
July 10, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28690971/materials-knowledge-systems-in-python-a-data-science-framework-for-accelerated-development-of-hierarchical-materials
#12
David B Brough, Daniel Wheeler, Surya R Kalidindi
There is a critical need for customized analytics that take into account the stochastic nature of the internal structure of materials at multiple length scales in order to extract relevant and transferable knowledge. Data driven Process-Structure-Property (PSP) linkages provide systemic, modular and hierarchical framework for community driven curation of materials knowledge, and its transference to design and manufacturing experts. The Materials Knowledge Systems in Python project (PyMKS) is the first open source materials data science framework that can be used to create high value PSP linkages for hierarchical materials that can be leveraged by experts in materials science and engineering, manufacturing, machine learning and data science communities...
March 2017: Integr Mater Manuf Innov
https://www.readbyqxmd.com/read/28690112/the-discovery-of-xy-sex-chromosomes-in-a-boa-and-python
#13
Tony Gamble, Todd A Castoe, Stuart V Nielsen, Jaison L Banks, Daren C Card, Drew R Schield, Gordon W Schuett, Warren Booth
For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1-3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]...
July 5, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28686798/multiplierz-v2-0-a-python-based-ecosystem-for-shared-access-and-analysis-of-native-mass-spectrometry-data
#14
William M Alexander, Scott B Ficarro, Guillaume Adelmant, Jarrod A Marto
The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data...
July 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28684712/decaf-discrimination-comparison-alignment-tool-for-2d-pharmacophores
#15
Marta M Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
Comparison of small molecules is a common component of many cheminformatics workflows, including the design of new compounds and libraries as well as side-effect predictions and drug repurposing. Currently, large-scale comparison methods rely mostly on simple fingerprint representation of molecules, which take into account the structural similarities of compounds. Methods that utilize 3D information depend on multiple conformer generation steps, which are computationally expensive and can greatly influence their results...
July 6, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28679794/modeling-the-costs-and-benefits-associated-with-the-evolution-of-endothermy-using-a-robotic-python
#16
J Alex Brashears, Ty C M Hoffman, Dale F DeNardo
Endothermy provides considerable benefits to an organism but requires large energy investment. To understand potential driving forces that would lead to the evolution of endothermy, it is important to understand the energy costs and potential benefits of intermediate steps between ectothermy and homeothermic endothermy as well as the influences of environmental conditions on energetic costs. However, efforts to examine intermediate conditions are greatly limited by the predominant natural dichotomy between ectothermy and endothermy...
July 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28666322/svm-dependent-pairwise-hmm-an-application-to-protein-pairwise-alignments
#17
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim Vranken
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666314/gpu-powered-model-analysis-with-pysb-cupsoda
#18
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/28659129/slmsuite-a-suite-of-algorithms-for-segmenting-genomic-profiles
#19
Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio, Alberto Magi
BACKGROUND: The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs can be achieved using microarray or second generation sequencing (SGS) data. Although these technologies are very different, the genomic profiles that they generate are mathematically very similar and consist of noisy signals in which a decrease or increase of consecutive data represent deletions or duplication of DNA...
June 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#20
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
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