SoftwareX最新文献_第2页

MyAphasia: A mobile application for the treatment of Aphasia in a hospital environment MyAphasia：一个在医院环境中治疗失语症的移动应用程序

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-28 DOI: 10.1016/j.softx.2025.102378

Andrés A. Sánchez-Cabrera , Pedro O. Rossel , Fabiola Aguirre-Delgado , Laura Aravena-Canese , Karen Chandía-Vásquez , Valeria Espejo-Videla , Valeria Herskovic

引用次数: 0

OCA: A Shiny web application for transparent overload compensation in higher education OCA：一个闪亮的web应用程序，用于高等教育中透明的过载补偿

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-25 DOI: 10.1016/j.softx.2025.102375

Dawit Aberra, Xiangyan Zeng, Chunhua Dong Mahon, Sanjeev Arora

引用次数: 0

Narrative Maps Visualization Tool (NMVT): An interactive narrative analytics system based on the narrative maps framework 叙事地图可视化工具（NMVT）：基于叙事地图框架的交互式叙事分析系统

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-25 DOI: 10.1016/j.softx.2025.102377

Brian Keith Norambuena

{"title":"Narrative Maps Visualization Tool (NMVT): An interactive narrative analytics system based on the narrative maps framework","authors":"Brian Keith Norambuena","doi":"10.1016/j.softx.2025.102377","DOIUrl":"10.1016/j.softx.2025.102377","url":null,"abstract":"<div><div>The <strong>Narrative Maps Visualization Tool</strong> (NMVT) is an interactive visual analytics system designed to help analysts understand complex narratives from collections of text documents. NMVT leverages graph-based representations to extract and visualize coherent storylines, showing how events connect over time. The system integrates advanced features including document clustering, coherence-based optimization, storyline extraction, and explainable AI components that provide interpretable insights into narrative connections. NMVT supports both directed analysis (connecting specific events) and exploratory analysis (discovering emerging storylines). By enabling analysts to make sense of large document collections, NMVT addresses critical challenges in intelligence analysis, computational journalism, and misinformation research, allowing users to effectively <em>connect the dots</em> between seemingly unrelated events. The system has been successfully demonstrated on news data by extracting coherent narrative structures that capture both main storylines and alternative perspectives. Case studies show that NMVT’s semantic interaction capabilities enable analysts to refine narratives based on domain expertise, while the explainable AI components increase trust in the system’s outputs.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102377"},"PeriodicalIF":2.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145159484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

UQpy Version 4.2: Uncertainty quantification with Python UQpy Version 4.2：使用Python进行不确定性量化

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-25 DOI: 10.1016/j.softx.2025.102364

Connor Krill, Ponkrshnan Thiagarajan, George D. Pasparakis, Somdatta Goswami, Dimitrios Tsapetis, Dimitris G. Giovanis, Michael D. Shields

引用次数: 0

Fed-batch bioreactor modeling 进料间歇生物反应器建模

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-25 DOI: 10.1016/j.softx.2025.102358

Tilen Gimpelj , Aleksandar Tošić

{"title":"Fed-batch bioreactor modeling","authors":"Tilen Gimpelj , Aleksandar Tošić","doi":"10.1016/j.softx.2025.102358","DOIUrl":"10.1016/j.softx.2025.102358","url":null,"abstract":"<div><div>This paper describes an open-source computational tool developed for the modeling and simulation of fed-batch bioreactors, particularly for processes employing Chinese Hamster Ovary (CHO) cells, which are integral to biopharmaceutical manufacturing. The software provides a platform for researchers and industry professionals to simulate bioreactor dynamics and investigate the impact of various operational parameters, such as nutrient supply rates, oxygen concentrations, and temperature, prior to physical experimentation. The tool enables users to generate predictions of critical variables including cell density, nutrient consumption, and product concentration profiles over time. These predictions are derived from a mathematical framework based on a system of ordinary differential equations solved using the Runge–Kutta method. A notable capability of the software is the import of experimental data and the application of the Nelder–Mead algorithm for parameter optimization, allowing for the calibration of the model against empirical findings, thereby enhancing its predictive accuracy. The software supports in silico experimentation, which can contribute to reducing the time, cost, and resources associated with optimizing bioreactor configurations and scaling up production processes. By providing a refined and adaptable framework, this instrument assists in improving the understanding of bioreactor dynamics, optimizing biopharmaceutical production methodologies, and correlating theoretical models with practical bioreactor operations. The software is available as an open-source project to promote its adoption and continued development within the scientific community.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102358"},"PeriodicalIF":2.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145159345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Care4Plant: Mobile application for informal caregivers Care4Plant：非正式护理人员的移动应用程序

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-25 DOI: 10.1016/j.softx.2025.102368

Bernardo Fernández-Zambrano , Carolina Fuentes , Pedro O. Rossel , Valeria Herskovic

{"title":"Care4Plant: Mobile application for informal caregivers","authors":"Bernardo Fernández-Zambrano , Carolina Fuentes , Pedro O. Rossel , Valeria Herskovic","doi":"10.1016/j.softx.2025.102368","DOIUrl":"10.1016/j.softx.2025.102368","url":null,"abstract":"<div><div>Informal caregivers provide long-term, unpaid support to patients – usually family or friends – with serious illnesses. Although caregiving is essential, it can have adverse effects, e.g. physical and emotional exhaustion. Digital applications are a cost-effective alternative to manage these effects. However, applications for caregivers are usually centered on skill building and education rather than well-being, and general-purpose stress management applications – besides not specifically considering caregivers – frequently change and do not usually incorporate social aspects. To design a caregiver-centered application, we analyzed caregiver needs, specifically focusing on well-being aspects. We present <em>Care4Plant</em>, an application designed to measure the emotional dimension of caregivers’ burden based on the Zarit Burden Questionnaire, and suggest a set of mood improvement tasks accordingly. <em>Care4Plant</em> features a virtual plant that represents informal caregivers’ emotional well-being, allowing them to care for the plant through actions intended to manage their mental health and reduce stress, and to share their plant with other caregivers through a social network represented by a greenhouse. We conducted an evaluation of <em>Care4Plant</em> with nine users over two weeks. The results indicated good levels of usability and demonstrated that the approach of motivating users through the virtual plant was well-received.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102368"},"PeriodicalIF":2.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145159346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CSTEapp: An interactive R-Shiny application of the covariate-specific treatment effect curve for visualizing individualized treatment rule CSTEapp：交互式R-Shiny应用协变量特异性治疗效果曲线，用于可视化个性化治疗规则

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-24 DOI: 10.1016/j.softx.2025.102352

Yi Zhou , Yuhao Deng , Yu-Shi Tian , Peng Wu , Wenjie Hu , Haoxiang Wang , Ewout Steyerberg , Xiao-Hua Zhou

{"title":"CSTEapp: An interactive R-Shiny application of the covariate-specific treatment effect curve for visualizing individualized treatment rule","authors":"Yi Zhou , Yuhao Deng , Yu-Shi Tian , Peng Wu , Wenjie Hu , Haoxiang Wang , Ewout Steyerberg , Xiao-Hua Zhou","doi":"10.1016/j.softx.2025.102352","DOIUrl":"10.1016/j.softx.2025.102352","url":null,"abstract":"<div><div>In precision medicine, deriving the individualized treatment rule (ITR) is crucial for recommending the optimal treatment based on patients’ baseline covariates. The covariate-specific treatment effect (CSTE) curve presents a graphical method to visualize an ITR within a causal inference framework. Recent advancements have enhanced the causal interpretation of the CSTE curves and provided methods for deriving simultaneous confidence bands for various study types. To facilitate the implementation of these methods and make ITR estimation more accessible, we developed CSTEapp, a web-based application built on the R Shiny framework. CSTEapp allows users to upload data and create CSTE curves through simple “point and click” operations, making it the first application for estimating the ITRs. CSTEapp simplifies the analytical process by providing interactive graphical user interfaces with dynamic results, enabling users to easily report optimal treatments for individual patients based on their covariates information. Currently, CSTEapp is applicable to studies with binary and time-to-event outcomes, and we continually expand its capabilities to accommodate other outcome types as new methods emerge. We demonstrate the utility of CSTEapp using real-world examples and simulation datasets. By making advanced statistical methods more accessible, CSTEapp empowers researchers and practitioners across various fields to advance precision medicine and improve patient outcomes.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102352"},"PeriodicalIF":2.4,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145159347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GAMMA_FLOW: Guided Analysis of Multi-label spectra by Matrix Factorization for Lightweight Operational Workflows GAMMA_FLOW：基于矩阵分解的轻量级操作工作流多标签谱的导向分析

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-24 DOI: 10.1016/j.softx.2025.102342

Viola Rädle , Tilman Hartwig , Benjamin Oesen , Emily Alice Kröger , Julius Vogt , Eike Gericke , Martin Baron

引用次数: 0

conjugate_map: A Python package for calculating geomagnetic conjugate points 计算地磁共轭点的Python包

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-23 DOI: 10.1016/j.softx.2025.102354

Kristina Collins , Michael Hartinger , Kelsey Zimmerman , Michelle Salzano , Angeline Burrell

{"title":"conjugate_map: A Python package for calculating geomagnetic conjugate points","authors":"Kristina Collins , Michael Hartinger , Kelsey Zimmerman , Michelle Salzano , Angeline Burrell","doi":"10.1016/j.softx.2025.102354","DOIUrl":"10.1016/j.softx.2025.102354","url":null,"abstract":"<div><div>The Earth’s magnetic field is dominated by the dipole moment, which magnetically connects the northern and southern hemispheres. Because ionospheric and magnetospheric plasmas preferentially move along magnetic field lines, local processes that affect the ionosphere or magnetosphere in one hemisphere can cause changes in the opposite hemisphere. The polar regions are uniquely valuable in geospace science, in part because much of the solar wind’s energy enters the system in polar regions and their magnetospheric, ionospheric, and atmospheric connections are markedly different from the lower latitudes. Geomagnetic conjugates are points in the northern and southern hemispheres linked by Earth’s magnetic field, including both points connected by closed magnetic field lines and points in open-field line regions that are in similar magnetic domains. Conjugate locations are both affected asymmetrically by external factors and have also been shown to alter each other’s environment on the order of minutes, which makes interhemispheric comparisons crucial to understanding the full dynamics of the geospace system. Here, we present <span>conjugate_map</span>, a Python library for flexible geomagnetic coordinate conversions that was designed to facilitate interhemispheric comparisons of geospace events and deployment of polar geospace instruments. As the fifth International Polar Year approaches in 2032–33, this work will help researchers to incorporate interhemispheric geospace investigations into the instrument planning process.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102354"},"PeriodicalIF":2.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

XNB: A package for Class-Specific Naive-Bayes classifier 特定于类的朴素贝叶斯分类器的包

IF 2.4 4区计算机科学

SoftwareX Pub Date : 2025-09-22 DOI: 10.1016/j.softx.2025.102347

Jesús S. Aguilar–Ruiz , Cayetano Romero–Vargas

{"title":"XNB: A package for Class-Specific Naive-Bayes classifier","authors":"Jesús S. Aguilar–Ruiz , Cayetano Romero–Vargas","doi":"10.1016/j.softx.2025.102347","DOIUrl":"10.1016/j.softx.2025.102347","url":null,"abstract":"<div><div>The Explainable Class-Specific Naive Bayes (<span>XNB</span>) package is a novel software tool for classification, specifically developed for high-dimensional data scenarios where interpretability is essential. <span>XNB</span> enhances the traditional Naive Bayes model through two core innovations. First, it replaces the restrictive Gaussian assumption with Kernel Density Estimation (KDE), enabling more flexible and accurate modeling of complex, non-Gaussian distributions. Second, it incorporates a class-specific feature selection strategy, which identifies distinct subsets of relevant variables associated with each class. This selection mechanism improves interpretability and reduces both dimensionality and feature redundancy. Empirical evaluations on genomic datasets show that <span>XNB</span> achieves competitive classification performance while using dramatically fewer features. The combination of accurate density estimation and class-aware, sparse feature selection results in a transparent classification framework. This makes the <span>XNB</span> package particularly valuable in domains such as biomedicine, where software tools that combine precision and explainability are critically needed.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"32 ","pages":"Article 102347"},"PeriodicalIF":2.4,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0