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  1. 1

    GraphPyRec: A novel graph-based approach for fine-grained Python code recommendation by Zong, Xing, Zheng, Shang, Zou, Haitao, Yu, Hualong, Gao, Shang

    ISSN: 0167-6423
    Published: Elsevier B.V 01.12.2024
    Published in Science of computer programming (01.12.2024)
    “… Significant progress has been made in code recommendation for static languages in recent years, but it remains challenging for dynamic languages like Python as accurately determining data flows…”
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    Journal Article
  2. 2

    Estimation of building project completion duration using a natural gradient boosting ensemble model and legal and institutional variables by Peiman, Farshad, Khalilzadeh, Mohammad, Shahsavari-Pour, Nasser, Ravanshadnia, Mehdi

    ISSN: 0969-9988, 1365-232X
    Published: Bradford Emerald Publishing Limited 28.03.2025
    “…PurposeEarned value management (EVM)–based models for estimating project actual duration (AD) and cost at completion using various methods are continuously…”
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    Journal Article
  3. 3

    Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC by Padovani, Francesco, Mairhörmann, Benedikt, Falter-Braun, Pascal, Lengefeld, Jette, Schmoller, Kurt M.

    ISSN: 1741-7007, 1741-7007
    Published: London BioMed Central 05.08.2022
    Published in BMC biology (05.08.2022)
    “…Background High-throughput live-cell imaging is a powerful tool to study dynamic cellular processes in single cells but creates a bottleneck at the stage of data analysis, due to the large amount…”
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    Journal Article
  4. 4

    Preliminary Experience and Learning Outcomes by Infusing Interactive and Active Learning to Teach an Introductory Programming Course in Python by Rahman, Md Mahmudur, Paudel, Roshan

    Published: Athens The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp) 01.01.2018
    “…) maps to a highly dynamic process (program execution). The program execution is typically illustrated using graphical PowerPoint lecture slides or by drawing diagrams on a whiteboard, which is tedious and error prone and requires huge effort…”
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    Conference Proceeding
  5. 5

    MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics by Haiman, Zachary B., Zielinski, Daniel C., Koike, Yuko, Yurkovich, James T., Palsson, Bernhard O.

    ISSN: 1553-7358, 1553-734X, 1553-7358
    Published: United States Public Library of Science 28.01.2021
    Published in PLoS computational biology (28.01.2021)
    “… MASSpy adds dynamic modeling tools to the COnstraint-Based Reconstruction and Analysis Python (COBRApy…”
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    Journal Article
  6. 6

    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

    ISSN: 1471-2105, 1471-2105
    Published: London BioMed Central 07.12.2023
    Published in BMC bioinformatics (07.12.2023)
    “…Background Variability in datasets is not only the product of biological processes…”
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    Journal Article
  7. 7

    Efficient Space–Time Reduced Order Model for Linear Dynamical Systems in Python Using Less than 120 Lines of Code by Kim, Youngkyu, Wang, Karen, Choi, Youngsoo

    ISSN: 2227-7390, 2227-7390
    Published: Basel MDPI AG 19.07.2021
    Published in Mathematics (Basel) (19.07.2021)
    “…A classical reduced order model (ROM) for dynamical problems typically involves only the spatial reduction of a given problem…”
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    Journal Article
  8. 8

    Deeptime: a Python library for machine learning dynamical models from time series data by Hoffmann, Moritz, Scherer, Martin, Hempel, Tim, Mardt, Andreas, de Silva, Brian, Husic, Brooke E, Klus, Stefan, Wu, Hao, Kutz, Nathan, Brunton, Steven L, Noé, Frank

    ISSN: 2632-2153, 2632-2153
    Published: Bristol IOP Publishing 01.03.2022
    Published in Machine learning: science and technology (01.03.2022)
    “… Deeptime is a general purpose Python library offering various tools to estimate dynamical models based on time-series data including conventional linear learning methods, such as Markov state models (MSMs…”
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    Journal Article
  9. 9

    Dynamic Generation of Python Bindings for HPC Kernels by Zhu, Steven, AlAwar, Nader, Erez, Mattan, Gligoric, Milos

    ISSN: 2643-1572
    Published: IEEE 01.11.2021
    “… A recent trend among scientists-prototyping applications in dynamic languages such as Python-created a gap between the applications and existing HPKs…”
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    Conference Proceeding
  10. 10

    PyGEE-SWToolbox: A Python Jupyter Notebook Toolbox for Interactive Surface Water Mapping and Analysis Using Google Earth Engine by Owusu, Collins, Snigdha, Nusrat J., Martin, Mackenzie T., Kalyanapu, Alfred J.

    ISSN: 2071-1050, 2071-1050
    Published: Basel MDPI AG 01.03.2022
    Published in Sustainability (01.03.2022)
    “… challenges. PyGEE-SWToolbox is a freely available Google Earth Engine-enabled open-source toolbox developed with Python to be run in Jupyter Notebooks that provides an easy-to-use graphical user interface (GUI…”
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    Journal Article
  11. 11

    3DDA: A Novel Python Toolkit to Analyze 3D‐Dynamic Contact Angles from Molecular Dynamics Simulations by Maslov, Andrea, Tiwari, Manish K., Seveno, David

    ISSN: 1438-1656, 1527-2648
    Published: 01.07.2025
    Published in Advanced engineering materials (01.07.2025)
    “… Herein, 3DDA, a Python‐based code that uses the 3D droplet geometry to determine contact angles and analyze dynamic changes during spreading processes at the nanoscale, is presented…”
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    Journal Article
  12. 12

    CRYSTALpytools: A Python infrastructure for the Crystal code by Camino, Bruno, Zhou, Huanyu, Ascrizzi, Eleonora, Boccuni, Alberto, Bodo, Filippo, Cossard, Alessandro, Mitoli, Davide, Ferrari, Anna Maria, Erba, Alessandro, Harrison, Nicholas M.

    ISSN: 0010-4655, 1879-2944
    Published: Elsevier B.V 01.11.2023
    Published in Computer physics communications (01.11.2023)
    “…CRYSTALpytools is an open source Python project available on GitHub that implements a user-friendly interface to the Crystal code for quantum-mechanical condensed matter simulations…”
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    Journal Article
  13. 13

    Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals by Combrisson, Etienne, Nest, Timothy, Brovelli, Andrea, Ince, Robin A. A., Soto, Juan L. P., Guillot, Aymeric, Jerbi, Karim

    ISSN: 1553-7358, 1553-734X, 1553-7358
    Published: United States Public Library of Science 29.10.2020
    Published in PLoS computational biology (29.10.2020)
    “… In particular, there is accumulating evidence that phase-amplitude coupling (PAC), a specific form of cross-frequency interaction, plays a key role in numerous cognitive processes…”
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    Journal Article
  14. 14

    PyCDFT: A Python package for constrained density functional theory by Ma, He, Wang, Wennie, Kim, Siyoung, Cheng, Man‐Hin, Govoni, Marco, Galli, Giulia

    ISSN: 0192-8651, 1096-987X, 1096-987X
    Published: Hoboken, USA John Wiley & Sons, Inc 30.07.2020
    Published in Journal of computational chemistry (30.07.2020)
    “…‐principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules…”
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    Journal Article
  15. 15

    A Python-based stochastic library for assessing geothermal power potential using the volumetric method in a liquid-dominated reservoir by Pocasangre, Carlos, Fujimitsu, Yasuhiro

    ISSN: 0375-6505, 1879-3576
    Published: Oxford Elsevier Ltd 01.11.2018
    Published in Geothermics (01.11.2018)
    “…•A Python-based stochastic library is presented for assessing geothermal potential…”
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    Journal Article
  16. 16
  17. 17

    Discovering Stochastic Dynamical Equations from Ecological Time Series Data by Nabeel, Arshed, Karichannavar, Ashwin, Palathingal, Shuaib, Jhawar, Jitesh, Brückner, David B, Raj M, Danny, Guttal, Vishwesha

    ISSN: 1537-5323, 1537-5323
    Published: United States 01.04.2025
    Published in The American naturalist (01.04.2025)
    “…AbstractTheoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways…”
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    Journal Article
  18. 18

    Glycosylator: a Python framework for the rapid modeling of glycans by Lemmin, Thomas, Soto, Cinque

    ISSN: 1471-2105, 1471-2105
    Published: London BioMed Central 22.10.2019
    Published in BMC bioinformatics (22.10.2019)
    “… The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N- linked glycosylation, plays an important role in the physiology of many living organisms…”
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    Journal Article
  19. 19

    PyCHAM (v2.1.1): a Python box model for simulating aerosol chambers by O'Meara, Simon Patrick, Xu, Shuxuan, Topping, David, Alfarra, M. Rami, Capes, Gerard, Lowe, Douglas, Shao, Yunqi, McFiggans, Gordon

    ISSN: 1991-9603, 1991-959X, 1991-962X, 1991-9603, 1991-962X
    Published: Katlenburg-Lindau Copernicus GmbH 02.02.2021
    Published in Geoscientific Model Development (02.02.2021)
    “…In this paper the CHemistry with Aerosol Microphysics in Python (PyCHAM) box model software for aerosol chambers is described and assessed against benchmark simulations for accuracy…”
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    Journal Article
  20. 20

    Verification of a Python-based TRANsport Simulation Environment for density-driven fluid flow and coupled transport of heat and chemical species by Kempka, Thomas

    ISSN: 1680-7359, 1680-7340, 1680-7359
    Published: Katlenburg-Lindau Copernicus GmbH 14.10.2020
    Published in Advances in geosciences (14.10.2020)
    “…Numerical simulation has become an inevitable tool for improving the understanding on coupled processes in the geological subsurface and its utilisation…”
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    Journal Article