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WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data
Published 2024“…Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generation of plots for monitoring the progress of large-scale simulations. Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble (WE) path sampling method, as implemented in the widely used WESTPA software package. …”
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Code
Published 2024“…<br>Note: The available code block "coi_types_integrity_issues.py" partially produces the data present in the CSV file present in the Data folder.…”
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Fluent Python nuggets. A brief presentation.
Published 2020“…Some nuggets of Python coding wisdom out of the book Fluent Python by Lucian Ramalho. …”
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Resolving Harvesting Errors in Institutional Repository Migration : Using Python Scripts with VS Code and LLM Integration.
Published 2025“…</li><li>Next, we provided GitHub Copilot with contextual information, file details, and analysis objectives as initial instructions to generate the Python code.…”
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Genomic view of archaeal and bacterial diversity in skeleton of coral Porites lutea and Isopora palifera
Published 2022“…<strong>Supplementary Data File:</strong> Microsoft Excel File with details of all the MAGs recovered in this work. …”
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PyGMT – Accessing and Integrating GMT with Python and the Scientific Python Ecosystem (AGU24, U12B-05)
Published 2024“…PyGMT integrates smoothly within the Scientific Python ecosystem. In addition to standard file formats such as ASCII and NetCDF files, common Pythonic data structures for tabular and grid data such as numpy.ndarray, pandas.DataFrame, geopandas.GeoDataFrame, and xarray.DataArray are supported. …”
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Real-Time Optical Imaging Acquisition and Processing in Python: A Practical Guide Using CAS: Code Repository
Published 2025“…</p><p dir="ltr">This repository contains code to accompany the paper:</p><p><br></p><p dir="ltr">Real-Time Optical Imaging Acquisition and Processing in Python: A Practical Guide Using CAS</p><p><br></p><p dir="ltr">Consult the paper for further details and explanation of what is included in this repository.…”
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sagetasks: a Python package for data and workflow orchestration in the cloud
Published 2022“…Notably, the GA4GH Workflow Execution Service (WES) presents an opportunity to minimize the amount of platform-specific code in favor of a common abstraction. …”