RealBench: A Repo-Level Code Generation Benchmark Aligned with Real-World Software Development Practices by RealBench RealBench (22275393)

“…<br><br><br></pre><p dir="ltr">This repository contains the implementation of **RealBench**, a comprehensive benchmark and evaluation framework for repository-level code aligned with real-world software development practices.…”

Predicting coding regions on unassembled reads, how hard can it be? - Genome Informatics 2024 by Amanda Clare (98717)

“…The locations and directions of the predictions on the reads are then combined with the information about locations and directions of the reads on the genome using Python code to produce detailed results regarding the correct, incorrect and alternative starts and stops with respect to the genome-level annotation.…”

Evaluation and Statistical Analysis Code for "Multi-Task Learning for Joint Fisheye Compression and Perception for Autonomous Driving" by Basem Ahmed (18127861)

“…</p><p dir="ltr">The code includes:</p><ul><li><a target="_blank"><code>evaluate_mtl.py</code></a>: The main script for evaluating the performance of the proposed deep learning models (JointGAD) and traditional codecs (HEVC, JPEG2000) on the Woodscape and Fisheye8k datasets. …”

Supporting data for "Interpreting complex ecological patterns and processes across differentscales using Artificial Intelligence" by Yifei Gu (9507104)

“…</p><p dir="ltr">Firstly, a Python package HSC3D, was developed to quantify habitat structural complexity (HSC) at the community level. …”

Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization by Eric W. Deutsch (13887)

“…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. …”

Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization by Eric W. Deutsch (13887)

“…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. …”

M-SGWR model by M. Naser Lessani (17817475)

“…<p dir="ltr">This project is related to the developemet of M-SGWR model. The repo contains all the necessary information, including the python code "M-SGWR", datasets and the instruction of how to reproduce the results presented in the article. …”

Excerpt from a provenance graph depicting the refinement process of a simulation model (SM1) during a simulation study. by Andreas Ruscheinski (7880759)

af3cli: Streamlining AlphaFold3 Input Preparation by Philipp Döpner (21028454)

“…With the release of AlphaFold3, modeling capabilities have expanded beyond protein structure prediction to embrace the inherent complexity of biomolecular systems, including nucleic acids, ions, small molecules, and their interactions. …”

Example provenance graph of exploring the difference between two simulation models by visualizing simulation data generated from two independent simulation experiments. by Andreas Ruscheinski (7880759)

Flowchart of the study participants. by Saeid Rasouli (20370998)

“…<div><p>Background</p><p>Optic neuritis (ON) can be an initial clinical presentation of multiple sclerosis This study aims to provide a practical predictive model for identifying at-risk ON patients in developing MS.…”

Feature importance of variables. by Saeid Rasouli (20370998)

“…<div><p>Background</p><p>Optic neuritis (ON) can be an initial clinical presentation of multiple sclerosis This study aims to provide a practical predictive model for identifying at-risk ON patients in developing MS.…”

Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing by John Docter (22772100)

Modeling organoid deformation. by Julien Laussu (3554030)

“…B: Schema presenting the three different types of controlled loads tested in the FEM model. …”

Extreme delta - pydeltaRCM models by Octria Adi Prasojo (10507373)

“…<p dir="ltr">The folder contains the Python codes (.ipynb) to run the pyDeltaRCM models of extreme events impact on delta morphodynamics across five climate regions, along with the modelling results (.nc) presented by the same authors in the manuscript.…”

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 by Junjie Zhang (355622)

“…</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.…”

Data and analysis code for manuscript "Preparations for ultra-high dose rate 25-90 MeV electron irradiation experiments with a compact, high-peak-current, X-band linear accelerator... by Haytham Effarah (11979509)

“…</p><p dir="ltr">The environment.yml file can create a conda virtual environment named "prep4vhee" with the required Python version and dependencies using the following conda command:</p><pre>conda env create -f environment.yml<br></pre><p dir="ltr">TOPAS input decks are also included in some folders with seeds set to reproduce Monte Carlo simulation results presented in the manuscript. …”

Dataset for the Modeling and Bibliometric Analysis of Business plan for Entrepreneurship by Shofie Galuh Amanda (22121604)

“…The analysis and visualization were carried out using R Biblioshiny for thematic mapping and trend topics, and Microsoft Excel for main information and annual publication production. For modeling, Python was applied to generate projection analyses of annual scientific production using polynomial regression. …”

Executable Books in Robotics by Murilo Marinho (21508857)

“…In this work, to showcase the results of the Open Research Fellowship 24-25 in the field of Robotics, I show one way to help bridge the theory-practice gap creating a fully open CC BY-NC-SA 4.0 licensed executable textbook in Python, based on Jupyter notebooks. …”

Fast, FAIR, and Scalable: Managing Big Data in HPC with Zarr by Alfonso Ladino (21447002)