SoftwareX最新文献_第10页

ZEN-garden: Optimizing energy transition pathways with user-oriented data handling

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102059

Jacob Mannhardt , Alissa Ganter , Johannes Burger , Francesco De Marco , Lukas Kunz , Lukas Schmidt-Engelbertz , Paolo Gabrielli , Giovanni Sansavini

引用次数: 0

tsdownsample: High-performance time series downsampling for scalable visualization

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102045

Jeroen Van Der Donckt, Jonas Van Der Donckt, Sofie Van Hoecke

{"title":"tsdownsample: High-performance time series downsampling for scalable visualization","authors":"Jeroen Van Der Donckt, Jonas Van Der Donckt, Sofie Van Hoecke","doi":"10.1016/j.softx.2025.102045","DOIUrl":"10.1016/j.softx.2025.102045","url":null,"abstract":"<div><div>Interactive line chart visualizations greatly enhance the effective exploration of large time series. Although downsampling has emerged as a well-established approach to enable efficient interactive visualization of large datasets, it is not an inherent feature in most visualization tools. Furthermore, there is no library offering a convenient interface for high-performance implementations of prominent downsampling algorithms. To address these shortcomings, we present <span>tsdownsample</span>, an open-source Python package specifically designed for CPU-based, in-memory time series downsampling. Our library focuses on performance and convenient integration, offering optimized implementations of leading downsampling algorithms. We achieve this optimization by leveraging low-level Single Instruction, Multiple Data (SIMD) instructions and multithreading capabilities in Rust. In particular, SIMD instructions were employed to optimize the argmin and argmax operations. This SIMD optimization, along with some algorithmic tricks, proved crucial in enhancing the performance of various downsampling algorithms. We evaluate the performance of <span>tsdownsample</span> and demonstrate its interoperability with an established visualization framework. Our performance benchmarks indicate that the algorithmic runtime of <span>tsdownsample</span> approximates the CPU’s memory bandwidth. This work marks a significant advancement in bringing high-performance time series downsampling to the Python ecosystem, enabling scalable visualization.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"29 ","pages":"Article 102045"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tsundoku: A Python toolkit for social network analysis

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2024.102008

Eduardo Graells-Garrido , Nicolás García , Andrés Carvallo

引用次数: 0

ParticleHolography.jl: Holographic particle measurement in Julia

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102056

Dai Nakai , Yohsuke Tanaka

引用次数: 0

biolutoxR: An R-Shiny package for easy performing data analysis of a toxicity test based on bacterial bioluminescence inhibition

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102061

Coralie Le Picard , Jérôme Cachot , Christelle Clérandeau , Arno Bringer , Benjamin Bellier

{"title":"biolutoxR: An R-Shiny package for easy performing data analysis of a toxicity test based on bacterial bioluminescence inhibition","authors":"Coralie Le Picard , Jérôme Cachot , Christelle Clérandeau , Arno Bringer , Benjamin Bellier","doi":"10.1016/j.softx.2025.102061","DOIUrl":"10.1016/j.softx.2025.102061","url":null,"abstract":"<div><div>In the 21st century, in the context of an environmental crisis, chemical pollution has become a major global concern. In addition to chemical analysis, many bioassays have been developed and have proved to be interesting tools for considerably improve our understanding of the effects of human activities on species and ecosystems. Compared with animal or plant bioassays, bacterial bioassays based on bioluminescence inhibition have the advantage of being relatively economical and reproducible. This toxicity test uses the bioluminescent metabolic response of bacteria exposed for a short time to a solution of interest in the aim of assessing and quantifying its toxicity. Although routine tools are available to pre-process the data obtained, to our knowledge no flexible research tool is available for the data analysis following these tests, which could limit the access to the results for novices or experienced people unfamiliar with data processing software. To overcome this lack of tools for this bioassay, an R-Shiny package is proposed to generalise data analysis following a toxicity test based on bacterial bioluminescence inhibition. The traditional paper-based working environment is reproduced digitally in this package, which ultimately facilitates data entry and cleaning, makes the creation of relevant dynamic graphs, and simplifies access to toxicity data (e.g. dose-response curve and median effective concentration, i.e. EC<sub>50</sub>). The aim of this tool is to provide the target community with a high-performance tool that can be used to obtain toxicity test results based on the inhibition of bacterial bioluminescence.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"29 ","pages":"Article 102061"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143093060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TIQA-MRI: Toolbox for Perceptual Image Quality Assessment of Magnetic Resonance Images

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102073

Igor Stępień

引用次数: 0

URSUS_UHI: URban SUStainability software for detection of unfavourable areas due to the Urban Heat Island effect

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2024.101997

Francisco Rodríguez-Gómez , José del Campo-Ávila , Domingo López-Rodríguez , Luis Pérez-Urrestarazu

引用次数: 0

ChestVolume: An R package and shiny app for analyzing chest expansion using 3D coordinate data

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102040

Patrick Wai-Hang Kwong , Eng Keong Lua , Clive Ho-Yin Wong , Allan Chak-Lun Fu , Fadi Mohammad Al Zoubi , Sharon Man-Ha Tsang

{"title":"ChestVolume: An R package and shiny app for analyzing chest expansion using 3D coordinate data","authors":"Patrick Wai-Hang Kwong , Eng Keong Lua , Clive Ho-Yin Wong , Allan Chak-Lun Fu , Fadi Mohammad Al Zoubi , Sharon Man-Ha Tsang","doi":"10.1016/j.softx.2025.102040","DOIUrl":"10.1016/j.softx.2025.102040","url":null,"abstract":"<div><div>ChestVolume is an R package and Shiny web application developed to facilitate the analysis of chest expansion using three-dimensional (3D) coordinate data obtained from optical motion capture systems. This software provides an end-to-end solution for respiratory analysis, including data preprocessing, marker position adjustment, volume calculation, and interactive visualization. The package includes functions for reformating marker data, adjusting marker positions, and calculating chest segment volumes using convex hull algorithms. Visualization tools allow users to explore chest expansion across time, providing a dynamic view of respiratory motion. The interactive Shiny app integrated with ChestVolume offers a user-friendly interface for individuals without advanced programming expertise, making chest volume analysis accessible to a wider audience. Users can upload 3D motion capture data, define custom chest segments, select specific time ranges, and visualize chest expansion patterns in both static and animated formats. These features enable researchers and clinicians to assess regional chest expansion and detect asymmetries in respiratory motion, which are crucial for understanding respiratory mechanics and evaluating conditions such as chronic obstructive pulmonary disease and spinal deformities. ChestVolume advances respiratory health research by providing an open-source, customizable, and accessible tool for the quantitative assessment of chest wall movement. The package supports personalized rehabilitation strategies by enabling the identification of asymmetric respiratory motion, facilitating targeted interventions to improve respiratory function, and ultimately contributing to enhanced clinical assessments and health outcomes.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"29 ","pages":"Article 102040"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HISAPS: High-order smoothing spline with automatic parameter selection and shape constraints

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102049

Peter H. Broberg , Esben Lindgaard , Asbjørn M. Olesen , Simon M. Jensen , Niklas K.K. Stagsted , Rasmus L. Bjerg , Riccardo Grosselle , Iñigo Urcelay Oca , Brian L.V. Bak

引用次数: 0

Code-Review-as-an-Educational-Service: A tool for Java code review in programming education

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-02-01 DOI: 10.1016/j.softx.2025.102048

Matthew Beattie, Moira Watson, Desmond Greer, Bee-Yen Toh, Zheng Li

{"title":"Code-Review-as-an-Educational-Service: A tool for Java code review in programming education","authors":"Matthew Beattie, Moira Watson, Desmond Greer, Bee-Yen Toh, Zheng Li","doi":"10.1016/j.softx.2025.102048","DOIUrl":"10.1016/j.softx.2025.102048","url":null,"abstract":"<div><div>High-quality source code is the foundation of successful and sustainable software development, while code review plays a crucial role in ensuring code quality. We place a special emphasis on the educational application of code review, aiming to assist novice students who are entry-level programmers establish industry-standard programming practices while reducing the likelihood of vulnerabilities and technical debt. Given that existing code review tools often require complex setups and are designed for large-scale, enterprise-level software projects, we advocate for the development of an easy-to-use, zero-configuration, and lightweight tool that is specifically tailored to the needs of educational environments. This paper reports our development of such a cloud-native code review tool as an educational service. Although still at the proof-of-concept stage, our internal and preliminary assessment has confirmed the promising usability and usefulness of this tool both for students (e.g., self-reviewing an individual exercise) and for educators (e.g., examining cohort exercises and prioritising teaching materials). By integrating this tool into our innovative project Automating Programming Education in Java, we believe that such an educational service would be able to make contributions to faster maturation of programming skills in students.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"29 ","pages":"Article 102048"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0