Search Results - Jupyter Notebook python script

A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts by Grotov, Konstantin, Titov, Sergey, Sotnikov, Vladimir, Golubev, Yaroslav, Bryksin, Timofey

“…: high number of code clones, low reproducibility, etc. In this work, we carry out a comparison between Python code written in Jupyter Notebooks and in traditional Python scripts…”
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Evaluation of analytic solutions for steady interface flow where the aquifer extends below the sea by Bakker, Mark, Miller, Anthony D., Morgan, Leanne K., Werner, Adrian D.

“…•Solution is implemented in Python script and Jupyter Notebook. A computational approach is presented for steady Dupuit interface flow where the aquifer extends below the sea…”
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TCGADownloadHelper: simplifying TCGA data extraction and preprocessing by Baumann, Alexandra Anke, Wolkenhauer, Olaf, Wolfien, Markus

“… We developed a pipeline integrating customizable Python scripts in a Jupyter…”
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A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts by Grotov, Konstantin, Titov, Sergey, Sotnikov, Vladimir, Golubev, Yaroslav, Bryksin, Timofey

“…: high number of code clones, low reproducibility, etc. In this work, we carry out a comparison between Python code written in Jupyter Notebooks and in traditional Python scripts…”
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PyCoM: a python library for large-scale analysis of residue–residue coevolution data by Bibik, Philipp, Alibai, Sabriyeh, Pandini, Alessandro, Dantu, Sarath Chandra

“… leveraging on biological and structural annotations already available in UniProt. Results We present a Python library, PyCoM, which enables users to query and analyze coevolution matrices and sequence alignments of 457…”
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Jupyter Cookbook: Over 75 Recipes to Perform Interactive Computing Across Python, R, Scala, Spark, JavaScript, and More by Toomey, Dan

“…Jupyter has garnered a strong interest in the data science community of late, as it makes common data processing and analysis tasks much simpler…”
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BioUML—towards a universal research platform by Kolpakov, Fedor, Akberdin, Ilya, Kiselev, Ilya, Kolmykov, Semyon, Kondrakhin, Yury, Kulyashov, Mikhail, Kutumova, Elena, Pintus, Sergey, Ryabova, Anna, Sharipov, Ruslan, Yevshin, Ivan, Zhatchenko, Sergey, Kel, Alexander

“…; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks…”
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Vizic: A Jupyter-based interactive visualization tool for astronomical catalogs by Yu, W., Carrasco Kind, M., Brunner, R.J.

“… In this paper we introduce Vizic, a Python visualization library that builds the connection between images and catalogs through an interactive map of the sky region…”
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sympl (v. 0.4.0) and climt (v. 0.15.3)—Towards a flexible framework for building model hierarchies in Python by Monteiro, Joy Merwin, McGibbon, Jeremy, Caballero, Rodrigo

“…) are an attempt to rethink climate modelling frameworks from the ground up. The aim is to use expressive data structures available in the scientific Python ecosystem along…”
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Collaborative and Reproducible Planetary Science Through the Europlanet GMAP JupyterHub Processing Environment by Nodjoumi, G., Brandt, C. H., Suárez‐Valencia, J. E., Luzzi, E., Valiante, M., Rossi, A. P.

“… This facilitates collaborative development and execution of Jupyter notebooks, Python scripts, and other tools among researchers and educators through a unified interface…”
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Jupyter in Computational Science by Fangohr, Hans, Kluyver, Thomas, DiPierro, Massimo

“… Before notebooks, a scientist working with Python code, for instance, might have used a mixture of script files and code typed into an interactive shell…”
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An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks by Braun, N, Hauth, T, Pulvermacher, C, Ritter, M

“… Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots…”
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litstudy: A Python package for literature reviews by Heldens, Stijn, Sclocco, Alessio, Dreuning, Henk, van Werkhoven, Ben, Hijma, Pieter, Maassen, Jason, van Nieuwpoort, Rob V.

“… Therefore, we present litstudy: a Python package that enables answering such questions using simple scripts or Jupyter notebooks…”
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Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics by Kohout, Pavel, Vasina, Michal, Majerova, Marika, Novakova, Veronika, Damborsky, Jiri, Bednar, David, Marek, Martin, Prokop, Zbynek, Mazurenko, Stanislav

“…Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among…”
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UniBioPAN: A Novel Universal Classification Architecture for Bioactive Peptides Inspired by Video Action Recognition by Wang, Ruihong, Liang, Xiao, Zhao, Yi, Xue, Wenjun, Liang, Guizhao

“…The classification of bioactive peptides is of great importance in protein biology, but there is still a lack of a universal and effective classifier. Inspired…”
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Teaching Python programming for bioinformatics with Jupyter notebook in the Post‐COVID ‐19 era by Gupta, Yash Munnalal, Kirana, Satwika Nindya, Homchan, Somjit, Tanasarnpaiboon, Supatcharee

“… To facilitate learning, we have modified the course to use Jupyter Notebook, which offers an alternative approach to writing custom scripts for basic DNA sequence analysis…”
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LegNet: a best-in-class deep learning model for short DNA regulatory regions by Penzar, Dmitry, Nogina, Daria, Noskova, Elizaveta, Zinkevich, Arsenii, Meshcheryakov, Georgy, Lando, Andrey, Rafi, Abdul Muntakim, de Boer, Carl, Kulakovskiy, Ivan V

“…Abstract Motivation The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex…”
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Tissue Forge: Interactive biological and biophysics simulation environment by Sego, T. J., Sluka, James P., Sauro, Herbert M., Glazier, James A.

“…Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to…”
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NGLview-interactive molecular graphics for Jupyter notebooks by Nguyen, Hai, Case, David A, Rose, Alexander S

“… Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client…”
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Volcanic and Seismic Source Modeling: An Open Tool for Geodetic Data Modeling by Trasatti, Elisa

“… theorem and the Markov chain Monte Carlo method. VSM can be executed as Python script, in Jupyter Notebook environments…”
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