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Analysis methods and code for very high-precision mass measurements of unstable isotopes by Karthein, J., Atanasov, D., Blaum, K., Lunney, D., Manea, V., Mougeot, M.

“…We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase…”
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A Study of Large Language Models in Detecting Python Code Violations by Mohammed Salih, Hekar A., Sarhan, Qusay I.

“… Common static code analysis tools for Python, such as Pylint and Flake8, are widely used to enforce code quality by detecting coding violations without executing the code…”
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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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SciPy 1.0: fundamental algorithms for scientific computing in Python by Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul

“… Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages…”
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DQC: A Python program package for differentiable quantum chemistry by Kasim, Muhammad F, Lehtola, Susi, Vinko, Sam M

“… Here, we present an open-source differentiable quantum chemistry simulation code and explore applications facilitated by automatic differentiation: (1) calculating molecular perturbation properties, (2) reoptimizing a basis set for hydrocarbons, (3) checking the stability of self-consistent field wave functions, and (4) predicting molecular properties via alchemical perturbations…”
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Principled and Practical Static Analysis for Python by Rak-Amnouykit, Ingkarat

“… Therefore, we first embark on a study to understand the current state of Python type systems…”
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Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3 by Bredesen-Aa, Bjørn André, Rehmsmeier, Marc

“… methods for the genome-wide prediction of candidate CREs. We here present Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences…”
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SBML2HYB: a Python interface for SBML compatible hybrid modeling by Pinto, José, Costa, Rafael S, Alexandre, Leonardo, Ramos, João, Oliveira, Rui

“…Abstract Summary Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML…”
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Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique by Yang, Hang, Lu, Xiaoxin, Chang, Jiaxing, Chang, Qing, Zheng, Wen, Chen, Zehua, Yi, Huiguang

“… These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges…”
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Pytim: A python package for the interfacial analysis of molecular simulations by Sega, Marcello, Hantal, György, Fábián, Balázs, Jedlovszky, Pál

“…Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations…”
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Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries by Beck, Armen G, Fine, Jonathan, Lam, Yu-Hong, Sherer, Edward C, Regalado, Erik L, Aggarwal, Pankaj

“…The screening of chemical libraries is an essential starting point in the drug discovery process. While some researchers desire a more thorough screening of…”
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Cardio PyMEA: A user-friendly, open-source Python application for cardiomyocyte microelectrode array analysis by Dunham, Christopher S., Mackenzie, Madelynn E., Nakano, Haruko, Kim, Alexis R., Nakano, Atsushi, Stieg, Adam Z., Gimzewski, James K.

“…Open source analytical software for the analysis of electrophysiological cardiomyocyte data offers a variety of new functionalities to complement closed-source, proprietary tools…”
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OTSun, a python package for the optical analysis of solar-thermal collectors and photovoltaic cells with arbitrary geometry by Cardona, Gabriel, Pujol-Nadal, Ramon

“… We present here the open source python package OTSun, which applies the Fresnel equations in their most general form, without further simplifications, and is suitable for the simulation of both solar…”
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ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data by Smit, Jochem H., Li, Yichen, Warszawik, Eliza M., Herrmann, Andreas, Cordes, Thorben

“… These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis…”
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PyISOLVER-A Fast Python OOP Implementation of LRDFIT Model by Yang, Fanghao, Menard, Jonathan E.

“… on the commercial software license. In this article, the original procedural program was ported from its commercial platform to an open-source Python platform and refactored into the object…”
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spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization by Bittremieux, Wout

“…Given the wide diversity in applications of biological mass spectrometry, custom data analyses are often needed to fully interpret the results of an experiment…”
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fv3gfs-wrapper: a Python wrapper of the FV3GFS atmospheric model by McGibbon, Jeremy, Brenowitz, Noah D., Cheeseman, Mark, Clark, Spencer K., Dahm, Johann P. S., Davis, Eddie C., Elbert, Oliver D., George, Rhea C., Harris, Lucas M., Henn, Brian, Kwa, Anna, Perkins, W. Andre, Watt-Meyer, Oliver, Wicky, Tobias F., Bretherton, Christopher S., Fuhrer, Oliver

“… As a result, researchers who use high-productivity languages for exploratory work often find these codes hard to understand, hard to modify, and hard to integrate with their analysis tools…”
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