Search Results - "Python programming language"

Array programming with NumPy by Harris, Charles R., Millman, K. Jarrod, van der Walt, Stéfan J., Gommers, Ralf, Virtanen, Pauli, Cournapeau, David, Wieser, Eric, Taylor, Julian, Berg, Sebastian, Smith, Nathaniel J., Kern, Robert, Picus, Matti, Hoyer, Stephan, van Kerkwijk, Marten H., Brett, Matthew, Haldane, Allan, del Río, Jaime Fernández, Wiebe, Mark, Peterson, Pearu, Gérard-Marchant, Pierre, Sheppard, Kevin, Reddy, Tyler, Weckesser, Warren, Abbasi, Hameer, Gohlke, Christoph, Oliphant, Travis E.

“…Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and…”
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads by Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, McCarthy, Shane A.

“…Background  PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have…”
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PF[DELTA]Screen - an open-source tool for automated PFAS feature prioritization in non-target HRMS data by Zweigle, Jonathan, Bugsel, Boris, Fabregat-Palau, Joel, Zwiener, Christian

“…Per- and polyfluoroalkyl substances (PFAS) are a huge group of anthropogenic chemicals with unique properties that are used in countless products and…”
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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations by Michaud-Agrawal, Naveen, Denning, Elizabeth J., Woolf, Thomas B., Beckstein, Oliver

“…MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein…”
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks by Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T., Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc

“…Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many…”
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Cooltools: Enabling high-resolution Hi-C analysis in Python by Abdennur, Nezar, Abraham, Sameer, Fudenberg, Geoffrey, Flyamer, Ilya M., Galitsyna, Aleksandra A., Goloborodko, Anton, Imakaev, Maxim, Oksuz, Betul A., Venev, Sergey V., Xiao, Yao

“…Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are…”
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SymPy: symbolic computing in Python by Meurer, Aaron, Smith, Christopher P., Paprocki, Mateusz, Čertík, Ondřej, Kirpichev, Sergey B., Rocklin, Matthew, Kumar, AMiT, Ivanov, Sergiu, Moore, Jason K., Singh, Sartaj, Rathnayake, Thilina, Vig, Sean, Granger, Brian E., Muller, Richard P., Bonazzi, Francesco, Gupta, Harsh, Vats, Shivam, Johansson, Fredrik, Pedregosa, Fabian, Curry, Matthew J., Terrel, Andy R., Roučka, Štěpán, Saboo, Ashutosh, Fernando, Isuru, Kulal, Sumith, Cimrman, Robert, Scopatz, Anthony

“…SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and…”
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PyPSA: Python for Power System Analysis by Brown, Thomas, Hörsch, Jonas, Schlachtberger, David

“…Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA…”
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SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses by Brown, Jason L., Bennett, Joseph R., French, Connor M.

“…SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most…”
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Comparison between fuzzy logic and water quality index methods: A case of water quality assessment in Ikare community, Southwestern Nigeria by Oladipo, Johnson O., Akinwumiju, Akinola S., Aboyeji, O.S., Adelodun, Adedeji A.

“…•Water quality index (WQI) and fuzzy logic inference (FLI) assessed water quality.•FLI is more efficient, accurate, and affordable than WQI.•Waters in Ikare…”
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Automated microstructural segmentation and grain size measurement of Al + SiC nanocomposites using advanced image processing techniques on backscattered electron images by Harikrishna, Katika, Nithin, Abeyram, Davidson, M.J.

“…Grain size analysis is crucial for understanding material properties, yet traditional manual methods are often time-consuming and labor-intensive. This study…”
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Pysteps: an open-source Python library for probabilistic precipitation nowcasting (v1.0) by Pulkkinen, Seppo, Nerini, Daniele, Pérez Hortal, Andrés A., Velasco-Forero, Carlos, Seed, Alan, Germann, Urs, Foresti, Loris

“…Pysteps is an open-source and community-driven Python library for probabilistic precipitation nowcasting, that is, very-short-range forecasting (0–6 h). The…”
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BindsNET: A Machine Learning-Oriented Spiking Neural Networks Library in Python by Hazan, Hananel, Saunders, Daniel J., Khan, Hassaan, Patel, Devdhar, Sanghavi, Darpan T., Siegelmann, Hava T., Kozma, Robert

“…The development of spiking neural network simulation software is a critical component enabling the modeling of neural systems and the development of…”
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SSR_(V)ibraProfiler: a Python package for accurate classification of varieties using SSRs with intra-variety specificity and inter-variety polymorphism by Jiang, Chenhao, Dong, Chuan, Wu, Zhenzhen, Shi, Chenyi, Ye, Qiannan, Wu, Xiaopei, Ma, Siyi, Wen, Yuming, Yu, Guoping, Wu, Jiasheng, Zhang, Chengjun

“…Simple sequence repeats (SSRs) are widely used as molecular markers; however, traditional development of SSR molecular markers heavily relies on experimental…”
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Analysis of the Application Efficiency of TensorFlow and PyTorch in Convolutional Neural Network by Novac, Ovidiu-Constantin, Chirodea, Mihai Cristian, Novac, Cornelia Mihaela, Bizon, Nicu, Oproescu, Mihai, Stan, Ovidiu Petru, Gordan, Cornelia Emilia

“…In this paper, we present an analysis of important aspects that arise during the development of neural network applications. Our aim is to determine if the…”
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chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling by Tessmer, Maxx H., Stoll, Stefan

“…Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular…”
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Eelbrain, a Python toolkit for time-continuous analysis with temporal response functions by Brodbeck, Christian, Das, Proloy, Gillis, Marlies, Kulasingham, Joshua P, Bhattasali, Shohini, Gaston, Phoebe, Resnik, Philip, Simon, Jonathan Z

“…Even though human experience unfolds continuously in time, it is not strictly linear; instead, it entails cascading processes building hierarchical cognitive…”
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CosinorPy: a python package for cosinor-based rhythmometry by Moskon, Miha

“…Background Even though several computational methods for rhythmicity detection and analysis of biological data have been proposed in recent years, classical…”
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Efficiency and accuracy of GPU-parallelized Fourier spectral methods for solving phase-field models by Boccardo, A.D., Tong, M., Leen, S.B., Tourret, D., Segurado, J.

“…Phase-field models are widely employed to simulate microstructure evolution during processes such as solidification or heat treatment. The resulting partial…”
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The Fusion Fuel Cycle Simulator — towards integrated dynamic process simulation of fusion fuel cycles by Teichmann, Tim, Schwenzer, Jonas, Day, Christian, Matsunaga, Yoshinao, McGrady, John, Kume, Yoshifumi, Baus, Colin, Konishi, Satoshi, Dashliborun, Amir Motamed

“…Kyoto Fusioneering in collaboration with Canadian Nuclear Laboratories, under the auspice of Fusion Fuel Cycles Inc. is developing the Fusion Fuel Cycle…”
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