Search Results - (( (state:in OR state) python code analysis ) OR ( state:ne python code analysis ))*

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

“… The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve…”
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Development of a New Thermal-Hydraulic Module for FRENETIC, a Code for the Multiphysics Analysis of Liquid Metal-Cooled Reactors by Lombardo, Antonino, Nallo, Giuseppe F., Abrate, Nicolò, Liu, Yapeng, Dulla, Sandra

“… The code performs steady-state and transient neutronic (NE) and TH coupled calculations while maintaining a relatively low computational cost thanks to the adoption of simplified physical models…”
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Avogadro: an advanced semantic chemical editor, visualization, and analysis platform by Hanwell, Marcus D, Curtis, Donald E, Lonie, David C, Vandermeersch, Tim, Zurek, Eva, Hutchison, Geoffrey R

“… Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API…”
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NuRadioMC: simulating the radio emission of neutrinos from interaction to detector by Glaser, C., García-Fernández, D., Nelles, A., Alvarez-Muñiz, J., Barwick, S. W., Besson, D. Z., Clark, B. A., Connolly, A., Deaconu, C., de Vries, K. D., Hanson, J. C., Hokanson-Fasig, B., Lahmann, R., Latif, U., Kleinfelder, S. A., Persichilli, C., Pan, Y., Pfendner, C., Plaisier, I., Seckel, D., Torres, J., Toscano, S., van Eijndhoven, N., Vieregg, A., Welling, C., Winchen, T., Wissel, S. A.

“… NuRadioMC is designed as a modern, modular Python-based framework, combining flexibility in detector design with user-friendliness…”
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REGALS : a general method to deconvolve X-ray scattering data from evolving mixtures by Meisburger, Steve P., Xu, Da, Ando, Nozomi

“…Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis…”
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PyLAT: Python LAMMPS Analysis Tools by Humbert, Michael T, Zhang, Yong, Maginn, Edward J

“… Here we describe a suite of open-source Python-based postprocessing routines we have developed called PyLAT…”
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python by Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary

“…Abstract Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes…”
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MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials by Singh, Sobhit, Lang, Logan, Dovale-Farelo, Viviana, Herath, Uthpala, Tavadze, Pedram, Coudert, François-Xavier, Romero, Aldo H.

“…The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij…”
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AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis by Isamura, Bienfait K., Lobb, Kevin A.

“…Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention…”
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VULCAN: An Open-source, Validated Chemical Kinetics Python Code for Exoplanetary Atmospheres by Tsai, Shang-Min, Lyons, James R., Grosheintz, Luc, Rimmer, Paul B., Kitzmann, Daniel, Heng, Kevin

“…We present an open-source and validated chemical kinetics code for studying hot exoplanetary atmospheres, which we name VULCAN…”
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Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics by Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

“…Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics…”
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Short communication: age2exhume – a MATLAB/Python script to calculate steady-state vertical exhumation rates from thermochronometric ages and application to the Himalaya by van der Beek, Peter, Schildgen, Taylor F.

“… datasets in such models remains challenging. Here, we present age2exhume, a thermal model in the form of a MATLAB or Python script, which can be used to rapidly obtain…”
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PHOTONAI—A Python API for rapid machine learning model development by Leenings, Ramona, Winter, Nils Ralf, Plagwitz, Lucas, Holstein, Vincent, Ernsting, Jan, Sarink, Kelvin, Fisch, Lukas, Steenweg, Jakob, Kleine-Vennekate, Leon, Gebker, Julian, Emden, Daniel, Grotegerd, Dominik, Opel, Nils, Risse, Benjamin, Jiang, Xiaoyi, Dannlowski, Udo, Hahn, Tim

“…PHOTONAI is a high-level Python API designed to simplify and accelerate machine learning model development…”
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pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods by Behdenna, Abdelkader, Colange, Maximilien, Haziza, Julien, Gema, Aryo, Appé, Guillaume, Azencott, Chloé-Agathe, Nordor, Akpéli

“… Results In this technical note, we present a new Python implementation of ComBat and ComBat-Seq…”
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Detecting Memory Errors in Python Native Code by Tracking Object Lifecycle with Reference Count by Ma, Xutong, Yan, Jiwei, Zhang, Hao, Yan, Jun, Zhang, Jian

“… To detect such problems, state-of-the-art approaches have made groundbreaking contributions to identifying inappropriate final refcount values before returning from native code to Python…”
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Nmrglue: an open source Python package for the analysis of multidimensional NMR data by Helmus, Jonathan J., Jaroniec, Christopher P.

“… When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number…”
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GPAW: An open Python package for electronic structure calculations by Mortensen, Jens Jørgen, Larsen, Ask Hjorth, Kuisma, Mikael, Ivanov, Aleksei V, Taghizadeh, Alireza, Peterson, Andrew, Haldar, Anubhab, Dohn, Asmus Ougaard, Schäfer, Christian, Jónsson, Elvar Örn, Hermes, Eric D, Nilsson, Fredrik Andreas, Kastlunger, Georg, Levi, Gianluca, Jónsson, Hannes, Häkkinen, Hannu, Fojt, Jakub, Kangsabanik, Jiban, Sødequist, Joachim, Lehtomäki, Jouko, Heske, Julian, Enkovaara, Jussi, Winther, Kirsten Trøstrup, Dulak, Marcin, Melander, Marko M, Ovesen, Martin, Louhivuori, Martti, Walter, Michael, Gjerding, Morten, Lopez-Acevedo, Olga, Erhart, Paul, Warmbier, Robert, Würdemann, Rolf, Kaappa, Sami, Latini, Simone, Boland, Tara Maria, Bligaard, Thomas, Skovhus, Thorbjørn, Susi, Toma, Maxson, Tristan, Rossi, Tuomas, Chen, Xi, Schmerwitz, Yorick Leonard A, Schiøtz, Jakob, Olsen, Thomas, Jacobsen, Karsten Wedel, Thygesen, Kristian Sommer

“…We review the GPAW open-source Python package for electronic structure calculations…”
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stk: A python toolkit for supramolecular assembly by Turcani, Lukas, Berardo, Enrico, Jelfs, Kim E.

“… stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes…”
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Snakes on a Spaceship - An Overview of Python in Heliophysics by Burrell, A.G., Halford, A., Klenzing, J., Stoneback, R. A., Morley, S. K., Annex, A. M., Laundal, K. M., Kellerman, A. C., Stansby, D., Ma, J.

“…Computational analysis has become ubiquitous within the heliophysics community. However, community standards for peer review of codes and analysis have lagged behind these developments…”
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The fast azimuthal integration Python library: pyFAI by Ashiotis, Giannis, Deschildre, Aurore, Nawaz, Zubair, Wright, Jonathan P., Karkoulis, Dimitrios, Picca, Frédéric Emmanuel, Kieffer, Jérôme

“… It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline…”
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