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Identification of Novel Microcystins Using High-Resolution MS and MSn with Python Code by Baliu-Rodriguez, David, Peraino, Nicholas J, Premathilaka, Sanduni H, Birbeck, Johnna A, Baliu-Rodriguez, Tomás, Westrick, Judy A, Isailovic, Dragan

“…Cyanotoxins called microcystins (MCs) are highly toxic and can be present in drinking water sources. Determining the structure of MCs is paramount because of…”
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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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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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scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data by Faure, Louis, Soldatov, Ruslan, Kharchenko, Peter V, Adameyko, Igor

“…Abstract Summary scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a…”
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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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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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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.

“…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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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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Python-based reduced order quadrature building code for fast gravitational wave inference by Qi, Hong, Raymond, Vivien

“… We describe a Python-based reduced order quadrature building code, pyroq, which builds the reduced order quadrature data needed to accelerate parameter estimation of gravitational waves…”
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Micki: A python-based object-oriented microkinetic modeling code by Hermes, Eric D, Janes, Aurora N, Schmidt, J R

“… This Python-based code is modular and object oriented, framing the development of microkinetic models in familiar chemical terms…”
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MEG and EEG data analysis with MNE-Python by Gramfort, Alexandre

“… As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple…”
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galpy: A python LIBRARY FOR GALACTIC DYNAMICS by Bovy, Jo

“…I describe the design, implementation, and usage of galpy, a python package for galactic-dynamics calculations…”
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Python code smells detection using conventional machine learning models by Sandouka, Rana, Aljamaan, Hamoud

“… This article proposes a Python code smell dataset for Large Class and Long Method code smells…”
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Pyleoclim: Paleoclimate Timeseries Analysis and Visualization With Python by Khider, Deborah, Emile‐Geay, Julien, Zhu, Feng, James, Alexander, Landers, Jordan, Ratnakar, Varun, Gil, Yolanda

“…We present a Python package geared toward the intuitive analysis and visualization of paleoclimate timeseries, Pyleoclim. The code is open‐source, object…”
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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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PBjam: A Python Package for Automating Asteroseismology of Solar-like Oscillators by Nielsen, M. B., Davies, G. R., Ball, W. H., Lyttle, A. J., Li 李坦, T. 达, Hall, O. J., Chaplin, W. J., Gaulme, P., Carboneau, L., Ong 王加, J. M. J. 冕, García, R. A., Mosser, B., Roxburgh, I. W., Corsaro, E., Benomar, O., Moya, A., Lund, M. N.

“… So far the process of performing an asteroseismic analysis of a star has remained somewhat esoteric and inaccessible to nonexperts…”
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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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pyMBE: The Python-based molecule builder for ESPResSo by Beyer, David, Torres, Paola B, Pineda, Sebastian P, Narambuena, Claudio F, Grad, Jean-Noël, Košovan, Peter, Blanco, Pablo M

“…We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG…”
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