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FibrilGen: A Python Package for Atomistic Modeling of Peptide β‑Sheet Nanostructures
Published 2025“…For <i>de novo</i> peptide-based nanomaterials that rely on the rational design of the peptide primary sequence, a systematic approach to computationally model the diverse and complex potential nanostructures formed by self-assembling peptides would be of considerable value. Here, we present FibrilGen, a bespoke Python package capable of building a broad range of cross-β morphologies at the atomic level. …”
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FibrilGen: A Python Package for Atomistic Modeling of Peptide β‑Sheet Nanostructures
Published 2025“…For <i>de novo</i> peptide-based nanomaterials that rely on the rational design of the peptide primary sequence, a systematic approach to computationally model the diverse and complex potential nanostructures formed by self-assembling peptides would be of considerable value. Here, we present FibrilGen, a bespoke Python package capable of building a broad range of cross-β morphologies at the atomic level. …”
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Evaluation and Statistical Analysis Code for "Multi-Task Learning for Joint Fisheye Compression and Perception for Autonomous Driving"
Published 2025“…</li></ul><p dir="ltr">These scripts are implemented in Python using the PyTorch framework and are provided to ensure the reproducibility of the experimental results presented in the manuscript.…”
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The codes and data for "A Graph Convolutional Neural Network-based Method for Predicting Computational Intensity of Geocomputation"
Published 2025“…The <b>innovations</b> and <b>steps</b> in Case 3, including data download, sample generation, and parallel computation optimization, were independently developed and are not dependent on the GeoCube’s code.</p><h2>Requirements</h2><p dir="ltr">The codes use the following dependencies with Python 3.8</p><ul><li>torch==2.0.0</li><li>torch_geometric==2.5.3</li><li>networkx==2.6.3</li><li>pyshp==2.3.1</li><li>tensorrt==8.6.1</li><li>matplotlib==3.7.2</li><li>scipy==1.10.1</li><li>scikit-learn==1.3.0</li><li>geopandas==0.13.2</li></ul><p><br></p>…”
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The codes and data for "A Graph Convolutional Neural Network-based Method for Predicting Computational Intensity of Geocomputation"
Published 2025“…The <b>innovations</b> and <b>steps</b> in Case 3, including data download, sample generation, and parallel computation optimization, were independently developed and are not dependent on the GeoCube’s code.</p><h2>Requirements</h2><p dir="ltr">The codes use the following dependencies with Python 3.8</p><ul><li>torch==2.0.0</li><li>torch_geometric==2.5.3</li><li>networkx==2.6.3</li><li>pyshp==2.3.1</li><li>tensorrt==8.6.1</li><li>matplotlib==3.7.2</li><li>scipy==1.10.1</li><li>scikit-learn==1.3.0</li><li>geopandas==0.13.2</li></ul><p><br></p>…”
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Code for the HIVE Appendicitis prediction modelRepository with LLM_data_extractor_optuna for automated feature extraction
Published 2025“…</p><p dir="ltr"><b>LLM Data Extractor optuna repo</b> is a Python framework for generating and evaluating clinical text predictions using large language models (LLMs) like <code>qwen2.5</code>. …”
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Efficient, Hierarchical, and Object-Oriented Electronic Structure Interfaces for Direct Nonadiabatic Dynamics Simulations
Published 2025“…We present a novel, flexible framework for electronic structure interfaces designed for nonadiabatic dynamics simulations, implemented in Python 3 using concepts of object-oriented programming. …”
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Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization
Published 2025“…We describe how Quetzal annotates spectra using the new Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) mzPAF standard for fragment ion peak annotation, including the Python-based code, a web-service end point that provides annotation services, and a web-based application for annotating spectra and producing publication-quality figures. …”
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Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization
Published 2025“…We describe how Quetzal annotates spectra using the new Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) mzPAF standard for fragment ion peak annotation, including the Python-based code, a web-service end point that provides annotation services, and a web-based application for annotating spectra and producing publication-quality figures. …”
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Tree file outputs from the phylogenetic analyses of the genus Python
Published 2025“…In addition, fossil evidence was appraised as supporting evidence for distribution but also to evaluate the hypothesis that large pythons (e.g., <u>></u> 6 m in body length) are restricted to warmer climatic zones, and this would be likely to influence their historical and present-day distributions. …”
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Data Sheet 1_osl-ephys: a Python toolbox for the analysis of electrophysiology data.docx
Published 2025“…This toolbox builds on top of the widely used MNE-Python package and provides unique analysis tools for magneto−/electro-encephalography (M/EEG) sensor and source space analysis, which can be used modularly. …”
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Automating Course Scheduling with Linear Programming and the Python PuLP Framework: First Steps
Published 2025“…<p dir="ltr">This article presents a pragmatic approach to automating course scheduling in an academic setting using linear programming.…”
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Research Data and Code on Characteristics and Drivers of Plant Diversity in Viaduct Footprint Spaces of a Mountainous, High-Density City—A Case Study of Central Chongqing
Published 2025“…</li><li>Derived data including calculated plant diversity metrics and environmental factor data.</li><li>R and python code used for statistical analysis.</li></ul><p dir="ltr">Data collection was conducted through on-site field surveys in the central urban area of Chongqing, China, from April to October 2024.…”