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Automated Estimation of Aquifer Parameters from Arbitrary‐Rate Pumping Tests in Python and MATLAB by Benson, David A.

“…Inspired by the analysis by Mishra et al. (2012) of variable pumping rate tests using piecewise…”
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VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models by Parker, Christopher, Nelson, Erik, Zhang, Tongli

“… VeVaPy includes four functional modules coded in Python, and the source code is publicly available…”
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ogs5py: A Python‐API for the OpenGeoSys 5 Scientific Modeling Package by Müller, Sebastian, Zech, Alraune, Heße, Falk

“…High‐performance numerical codes are an indispensable tool for hydrogeologists when modeling subsurface flow and transport systems…”
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Visualization of Aqueous Geochemical Data Using Python and WQChartPy by Yang, Jing, Liu, Honghua, Tang, Zhonghua, Peeters, Luk, Ye, Ming

“… This method note presents WQChartPy, an open‐source Python package developed to plot a total of 12 diagrams for analysis of aqueous geochemical data…”
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SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data by Li, Chang, Ma, Kevin, Xu, Nicole, Fu, Chenjian, He, Andrew, Liu, Xiaoming, Bai, Yongsheng

“… In this study, we updated SNPAAMapper, a variant annotation pipeline by converting perl codes to python for generating annotation output with an improved computational efficiency and updated…”
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Pastas: Open Source Software for the Analysis of Groundwater Time Series by Collenteur, Raoul A., Bakker, Mark, Caljé, Ruben, Klop, Stijn A., Schaars, Frans

“…), and the detection of trends and outliers. Pastas is a new and open source Python package for the analysis of hydrogeological time series…”
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Writing Analytic Element Programs in Python by Bakker, Mark, Kelson, Victor A

“… With the advent of the Python object-oriented programming language, it has become relatively easy to write analytic element programs…”
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A Generic Closed‐Loop Contaminant Treatment System Package for MODFLOW 6 by White, Jeremy T., Ewing, John E., Ruskauff, Greg, Rashid, Helal

“…We present a contaminant treatment system (CTS) package for MODFLOW 6 that facilitates the simulation of pump‐and‐treat systems for groundwater remediation…”
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Coupling a Borehole Thermal Model and MT3DMS to Simulate Dynamic Ground Source Heat Pump Efficiency by Zong, Yifei, Valocchi, Albert J., Lin, Yu‐Feng F.

“… In our approach, MT3DMS is the simulator for the two‐dimensional field‐scale heat transport, while new Python modules are developed to analytically solve the thermal transfer process within boreholes and interface iteratively with MT3DMS…”
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Percolation theory using Python by Malthe-Sørenssen, Anders

“… Readers will learn how to generate, analyze, and comprehend data and models, with detailed theoretical discussions complemented by accessible computer codes…”
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lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R by Khleborodova, Asya, Gamboa-Tuz, Samuel D, Ramos, Marcel, Segata, Nicola, Waldron, Levi, Oh, Sehyun

“…Summary LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal…”
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Decoding the JAK-STAT Axis in Colorectal Cancer with AI-HOPE-JAK-STAT: A Conversational Artificial Intelligence Approach to Clinical–Genomic Integration by Yang, Ei-Wen, Waldrup, Brigette, Velazquez-Villarreal, Enrique

“…: AI-HOPE-JAK-STAT combines large language models (LLMs), a natural language-to-code engine, and harmonized public CRC datasets from cBioPortal…”
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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial by Smith, Matthew J., Mansournia, Mohammad A., Maringe, Camille, Zivich, Paul N., Cole, Stephen R., Leyrat, Clémence, Belot, Aurélien, Rachet, Bernard, Luque‐Fernandez, Miguel A.

“…The main purpose of many medical studies is to estimate the effects of a treatment or exposure on an outcome. However, it is not always possible to randomize…”
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LiPydomics: A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data by Ross, Dylan H, Cho, Jang Ho, Zhang, Rutan, Hines, Kelly M, Xu, Libin

“… Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification…”
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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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Digitizing ECG image: A new method and open-source software code by Fortune, Julian D., Coppa, Natalie E., Haq, Kazi T., Patel, Hetal, Tereshchenko, Larisa G.

“… asynchronous ECG leads.•We provided open-source Python code that will facilitate further development of the tool…”
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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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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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