SoftwareX最新文献

{"title":"topoEEG: An Python-framework for analyzing EEG data in neurodegeneratives disease through Topological Deep Learning","authors":"Miriam Esteve ,&nbsp;Alejandro Martinez-Gracia ,&nbsp;Jesus J. Rodríguez-Sala ,&nbsp;Antonio Falcó","doi":"10.1016/j.softx.2025.102222","DOIUrl":"10.1016/j.softx.2025.102222","url":null,"abstract":"<div><div><strong>topoEEG</strong> is a Python framework designed for advanced EEG analysis, combining the MNE library with Topological Deep Learning (TDL) to enhance insights into neuroimaging, particularly for neurodegenerative diseases such as Alzheimer’s. The framework preprocesses EEG data by removing artifacts using Independent Component Analysis (ICA) and performs Power Spectral Density (PSD) analysis to identify critical frequency bands. By incorporating TDL, <strong>topoEEG</strong> uncovers topological features that traditional methods often overlook, offering deeper insights into neural activity. Unlike other standalone tools, it provides a unified solution, enhancing the accessibility of sophisticated analytics and supporting research in the diagnosis and understanding of neurodegenerative diseases.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102222"},"PeriodicalIF":2.4,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329623","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}

{"title":"IQM-Vis: A user-centric python toolbox for visualising and evaluating image quality metrics","authors":"M. Clifford ,&nbsp;A. Hepburn ,&nbsp;R. Kleinlein ,&nbsp;J. Vila-Tomás ,&nbsp;P. Hernández-Cámara ,&nbsp;P. Dauden ,&nbsp;N. Lepora ,&nbsp;V. Laparra ,&nbsp;R. Santos-Rodríguez","doi":"10.1016/j.softx.2025.102225","DOIUrl":"10.1016/j.softx.2025.102225","url":null,"abstract":"<div><div>Image Quality Metrics (IQMs) assess differences between images where human judgements are too expensive or infeasible due to the number of evaluations needed. Although a multitude of IQMs have been proposed in the literature, none are considered flawless. Therefore, it is crucial to understand their limitations by evaluating their suitability for different application domains. This type of evaluation is both qualitative and quantitative, lending itself best to interactive graphical tools. To this end, we created IQM-Vis, the first open source toolbox dedicated to analysing IQMs, visualising image distortions and conducting human image perception experiments, all through a simple Python interface.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102225"},"PeriodicalIF":2.4,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329622","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}

{"title":"OSP-SAP: A MATLAB graphical user interface for optimal sensor placement using SAP2000","authors":"Antonio S. López-Cuervo ,&nbsp;Enrique García-Macías ,&nbsp;Rafael Castro-Triguero ,&nbsp;Juan Chiachío","doi":"10.1016/j.softx.2025.102216","DOIUrl":"10.1016/j.softx.2025.102216","url":null,"abstract":"<div><div>An optimal placement of sensors is key for structural modal identification since it critically determines the quality of the estimated modal properties. To facilitate this task, this paper presents OSP-SAP, a MATLAB-based graphical user interface designed for Optimal Sensor Placement (OSP) using SAP2000 finite element models. The software integrates four different optimization algorithms to determine optimal sensor configurations while providing intuitive visualization tools. Additionally, OSP-SAP streamlines practical implementation by allowing users to export the generated optimal configurations to AutoCAD and generate Word reports, making OSP more accessible to researchers and practitioners.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102216"},"PeriodicalIF":2.4,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321254","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}

{"title":"madmpy: A Python library for creating and validating Data Management Plans","authors":"Alberto Ballesteros-Rodríguez ,&nbsp;Miguel-Ángel Sicilia ,&nbsp;Elena García-Barriocanal","doi":"10.1016/j.softx.2025.102215","DOIUrl":"10.1016/j.softx.2025.102215","url":null,"abstract":"<div><div>Data Management Plans (DMPs) are documents that describe the data used and produced during the course of research projects. Machine-actionable DMPs (maDMPs) are plans written in computer-readable formats. They are designed to support the automation of data-generation processes in scientific research. The <span>madmpy</span> Python package validates maDMPs that follow any version of the RDA DMP Common Standard. These plans can be written in JSON format or built programmatically. It also supports institution- or domain-specific extensions and additional validations that adhere to the standard. The library serves as a building block for research data engineering workflows. It promotes data management and accountability through the use of structured DMPs.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102215"},"PeriodicalIF":2.4,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144298774","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}

{"title":"DIC2Abaqus: Calculating mixed-mode stress intensity factors from 2D and 3D-stereo displacement fields","authors":"Abdalrhaman Koko ,&nbsp;James Marrow","doi":"10.1016/j.softx.2025.102231","DOIUrl":"10.1016/j.softx.2025.102231","url":null,"abstract":"<div><div>Evaluating the conditions for crack propagation under static and cyclic loads is critical for predicting the lifespan of engineering components, particularly in the energy and transport industries. Digital Image Correlation (DIC) provides precise displacement field measurements that can be used to calculate strain energy release rates and stress intensity factors (SIFs), but integrating DIC data into computer-aided engineering (CAE) software like Abaqus, a widely used finite element package, remains challenging. This paper introduces DIC2Abaqus, a freely available MATLAB-based tool that automates DIC data processing in Abaqus to extract material properties in isotropic and anisotropic elastic and elastoplastic materials. It employs the <em>J</em>-integral and interaction integral methods to compute mixed-mode SIFs, including mode III, without requiring a predefined specimen geometry or applied loads. It supports 2D and 3D-stereo DIC data and streamlines the process from geometry creation to job submission and post-processing. Validation against analytical and experimental results confirms its accuracy and reliability. By taking fracture mechanics analyses beyond ISO and ASTM <span><span>standards</span><svg><path></path></svg></span>, DIC2Abaqus offers a versatile, efficient, and accessible simulation tool for industry, research, and education.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102231"},"PeriodicalIF":2.4,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279250","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}

{"title":"A complete and open Simulink model of the Tennessee Eastman process (COSTEP)","authors":"Johandri Vosloo ,&nbsp;Kenneth R. Uren ,&nbsp;George van Schoor","doi":"10.1016/j.softx.2025.102217","DOIUrl":"10.1016/j.softx.2025.102217","url":null,"abstract":"<div><div>The Tennessee Eastman process serves as a benchmark system for the evaluation of fault diagnosis techniques. Current simulator implementations are available in FORTRAN and in a C-mex S-function in MATLAB. The C-mex file is a conversion of the FORTRAN code to C for implementation in MATLAB. Both implementations have the limitation that not all the variables and parameters are directly accessible. Hence, a complete and open Tennessee Eastman process simulator was developed in Simulink to allow for total access to all parameters and variables and better Simulink integration. This implementation will give researchers more freedom towards the design of control and fault diagnosis techniques.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102217"},"PeriodicalIF":2.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144270336","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}

{"title":"Tab2KGWiz: Interactive assistant for mapping tabular data to knowledge graphs","authors":"Z. Chen ,&nbsp;J. Chamorro-Padial ,&nbsp;J.M. López-Gil ,&nbsp;R.M. Gil ,&nbsp;R. García","doi":"10.1016/j.softx.2025.102221","DOIUrl":"10.1016/j.softx.2025.102221","url":null,"abstract":"<div><div>The reusability of research data is a key aspect of science development. According to FAIR principles, to make data reusable, it is required to make it interoperable. In this work, we present Tab2KGWiz, a software designed to enrich tabular data by adding contextual information formalized as Knowledge Graphs and based on ontologies. The metadata to automate the mapping of tabular datasets into Knowledge Graphs is generated interactively by the users under the guidance of Tab2KGWiz. It is then stored and exported into the YARRRML format, which can then be reused by tools that automate the mapping from tabular to semantic graph data based on the RDF standard. Tab2KGWiz is designed to help researchers enrich the metadata of their dataset by using an intuitive graphical user interface. The software is designed with a microservice architecture with a Java Spring back-end and a React front-end. Our application helps researchers and other data-sharing actors make their data easier to discover, access, and integrate, fostering collaboration and innovation.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102221"},"PeriodicalIF":2.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144270335","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}

{"title":"SolarQGIS: A QGIS application for calculating solar radiation on 3D vector GIS data","authors":"Mateusz Ilba","doi":"10.1016/j.softx.2025.102230","DOIUrl":"10.1016/j.softx.2025.102230","url":null,"abstract":"<div><div>The transition toward renewable energy sources is critical for urban sustainability. Solar energy, as a primary resource, necessitates accurate tools for potential assessment. Existing methodologies that utilize raster or vector data exhibit limitations, including restricted vertical surface analysis, inadequate resolution, and computational challenges. To address these shortcomings, the SolarQGIS application, built upon the QGIS, has been developed. This application facilitates solar radiation analysis on any 3D vector surface, incorporating empirical meteorological data and terrain characteristics. SolarQGIS provides a wide range of functionalities, enabling analysis from individual building scales to extensive urban environments, and can be used for both scientific and commercial purposes, including photovoltaic sector and public administration applications.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102230"},"PeriodicalIF":2.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261509","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}

{"title":"ESAC (EQ-SANS Assisting Chatbot): Application of large language models and retrieval-augmented generation for enhanced user experience at EQ-SANS","authors":"Changwoo Do,&nbsp;Gergely Nagy,&nbsp;William T. Heller","doi":"10.1016/j.softx.2025.102191","DOIUrl":"10.1016/j.softx.2025.102191","url":null,"abstract":"<div><div>Neutron scattering experiments have played vital roles in exploring materials properties in the past decades. While user interfaces have been improved over time, neutron scattering experiments still require specific knowledge or training by an expert due to the complexity of such advanced instrumentation and the limited number of experiments each person may perform each year. This paper introduces an innovative chatbot application that leverages Large Language Models(LLM) and Retrieval-Augmented Generation (RAG) technologies to significantly enhance the user experience at the EQ-SANS, a small-angle neutron scattering instrument at the Spallation Neutron Source of Oak Ridge National Laboratory. Through a user-centric design approach, the EQ-SANS Assisting Chatbot (ESAC) serves as an interactive reference for users, thereby facilitating the use of the instrument by visiting scientists. By bridging the gap between the users of EQ-SANS and the control systems required to perform their experiments, the ESAC sets a new standard for interactive learning and support for the scientific community using large-scale scientific facilities.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102191"},"PeriodicalIF":2.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144254568","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}

{"title":"scSpatialSIM: a simulator of spatial single-cell molecular data","authors":"Alex C. Soupir ,&nbsp;Julia Wrobel ,&nbsp;Jordan H. Creed ,&nbsp;Oscar E. Ospina ,&nbsp;Christopher M. Wilson ,&nbsp;Brandon J. Manley ,&nbsp;Lauren C. Peres ,&nbsp;Brooke L. Fridley","doi":"10.1016/j.softx.2025.102223","DOIUrl":"10.1016/j.softx.2025.102223","url":null,"abstract":"<div><div>The increasing use of spatial molecular technologies such as multiplex immunofluorescence (mIF) and spatial transcriptomics (SRT) has driven the need for robust statistical methods to analyze the spatial architecture of tissues. However, a lack of consensus on “gold standard” approaches present challenges for benchmarking and comparison. To address this gap, we developed “scSpatialSIM”, an <em>R</em> package for simulating biologically realistic spatial single-cell molecular data. “scSpatialSIM” enables users to efficiently simulate single-cell spatial patterns without requiring reference datasets, incorporating features such as cell clustering, cell co-localization, tissue compartments, and tissue holes. Additionally, the package supports simulation of both categorical data (e.g., cell phenotypes) and continuous values (e.g., protein expression or gene expression), and integrates with other <em>R</em> packages for downstream spatial analyses. To demonstrate its utility, we applied “scSpatialSIM” to benchmark univariate point pattern summary functions, including Ripley’s K(<em>r</em>), nearest neighbor G(<em>r</em>), and pair correlation g(<em>r</em>), across simulated scenarios. The results showed that Ripley’s K(<em>r</em>) consistently detected clustering across multiple radii, outperforming other methods in sensitivity and robustness. While scSpatialSIM is limited to simulating cell clustering and co-localization rather than broader tissue-level sub-domains, it provides a flexible and scalable framework for generating diverse spatial data. The development of scSpatialSIM facilitates comparative evaluation of spatial statistics and enables researchers to explore hypothetical scenarios at scale, advancing the development of novel methods to characterize the spatial organization of tissues. By providing a platform for spatial simulation, scSpatialSIM supports innovation in spatial molecular research and fosters new insights into tissue architecture and cellular interactions.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102223"},"PeriodicalIF":2.4,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144229691","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}