SoftwareXPub Date : 2025-07-22DOI: 10.1016/j.softx.2025.102255
Xavier Michalet
{"title":"AlliGator: Open source fluorescence lifetime imaging analysis in G","authors":"Xavier Michalet","doi":"10.1016/j.softx.2025.102255","DOIUrl":"10.1016/j.softx.2025.102255","url":null,"abstract":"<div><div>Fluorescence Lifetime Imaging (FLI) is a technique recording the temporal decay of fluorescence emission at every pixel of an image. Analyzing the information embedded in FLI dataset requires either fitting the decay to a predefined model using nonlinear least-square fit or maximum likelihood estimation, or projecting the decay on an orthogonal basis of periodic functions as in phasor analysis. AlliGator is a Windows open source software (BSD license) implementing these approaches in a user-friendly graphical user interface (GUI) and offering numerous unique features such as Förster Resonant Energy Transfer (FRET) stoichiometry analysis, or the creation of maps of lifetime-derived quantities such as membrane potential. It leverages the unique ability of the LabVIEW graphical programming language (G) to design feature-rich GUI, and supports user-developed plugins written in python to extend its native capabilities.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102255"},"PeriodicalIF":2.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144679547","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}
SoftwareXPub Date : 2025-07-21DOI: 10.1016/j.softx.2025.102250
Francisco Ortin , Oscar Rodriguez-Prieto , Miguel Garcia
{"title":"Introspector: A general-purpose tool for visualizing and comparing runtime object structures on the Java platform","authors":"Francisco Ortin , Oscar Rodriguez-Prieto , Miguel Garcia","doi":"10.1016/j.softx.2025.102250","DOIUrl":"10.1016/j.softx.2025.102250","url":null,"abstract":"<div><div>Understanding the runtime behavior of complex software systems requires dynamic analysis beyond traditional static inspection techniques. Modern applications rely on intricate hierarchies of interconnected objects, making runtime structure analysis crucial for debugging and software comprehension. Traditional approaches such as debuggers, logging, and memory profilers often require significant manual effort to visualize and compare complex object data structures. To address these limitations, we implemented Introspector, a general-purpose tool that provides interactive visualization of any runtime object data structure for applications written in any language compiled to the Java platform. Unlike existing tools, Introspector does not require source code access, supports real-time visualization, and enables automated structural comparisons of object graphs at different execution points. Additionally, it allows for report generation in both text and HTML formats. Introspector is designed to be lightweight, integrating seamlessly into any Java application via its JAR file, not requiring entering debug mode with the corresponding runtime performance overhead of other JDPA-based approaches. Introspector has been successfully applied in multiple domains, including software development, education, and scientific research. It has enabled developers to compare evolving data structures during program execution, educators to visually demonstrate complex programming concepts, and researchers to inspect object data structures such as deep neural networks and biological data structures.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102250"},"PeriodicalIF":2.4,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144672104","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}
SoftwareXPub Date : 2025-07-19DOI: 10.1016/j.softx.2025.102248
Sergio Morales , Robert Clarisó , Jordi Cabot
{"title":"LangBiTe: An open-source platform to automate bias testing of large language models","authors":"Sergio Morales , Robert Clarisó , Jordi Cabot","doi":"10.1016/j.softx.2025.102248","DOIUrl":"10.1016/j.softx.2025.102248","url":null,"abstract":"<div><div>The popularity of large language models (LLMs) raises concerns about their potential biases and their impact on society. Typically, those models are trained on a vast amount of data scrapped from forums, websites, social media and other internet sources, which may instill harmful and discriminating behavior into the model. To address this issue, we present <em>LangBiTe</em>, a testing platform to systematically assess the presence of biases within an LLM. Sociologists, ethicists and other researchers can leverage <em>LangBite</em> to execute their studies, by automatically generating and executing tests according to a set of user-defined ethical requirements and a scenario definition. Each test consists of a prompt fed into the LLM and a corresponding test oracle that scrutinizes the LLM’s response for the identification of biases. <em>LangBite</em> provides users with the bias evaluation of LLMs, and end-to-end traceability between the initial ethical requirements and the insights obtained.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102248"},"PeriodicalIF":2.4,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663637","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}
SoftwareXPub Date : 2025-07-19DOI: 10.1016/j.softx.2025.102253
Piotr Białas , Piotr Korcyl , Tomasz Stebel , Dawid Zapolski
{"title":"NeuMC — A package for neural sampling for lattice field theories","authors":"Piotr Białas , Piotr Korcyl , Tomasz Stebel , Dawid Zapolski","doi":"10.1016/j.softx.2025.102253","DOIUrl":"10.1016/j.softx.2025.102253","url":null,"abstract":"<div><div>We present the <span>NeuMC</span> software package aimed at facilitating the research on neural samplers in lattice field theories. Neural samplers based on normalizing flows are becoming increasingly popular in the context of Monte–Carlo simulations as they can effectively approximate target probability distributions, possibly alleviating some shortcomings of the Markov chain Monte–Carlo methods such as critical slowing down. Our package provides tools to create such samplers for two-dimensional field theories and is based on a popular <span>PyTorch</span> package.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102253"},"PeriodicalIF":2.4,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663636","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}
SoftwareXPub Date : 2025-07-18DOI: 10.1016/j.softx.2025.102260
Ali Forootani , Danial Esmaeili Aliabadi , Daniela Thrän
{"title":"Bio-Eng-LLM AI Assist: A modular chatbot platform for interdisciplinary research and education","authors":"Ali Forootani , Danial Esmaeili Aliabadi , Daniela Thrän","doi":"10.1016/j.softx.2025.102260","DOIUrl":"10.1016/j.softx.2025.102260","url":null,"abstract":"<div><div>This article presents <span>Bio-Eng-LLM</span> <span>AI</span> <span>chatbot</span> Assist, a versatile platform designed to support interactive learning and research across multiple disciplines. Initially developed for biomass research, the system’s capabilities have since expanded to serve broader educational and scientific domains. It integrates large language models (<span>LLM</span>s) with advanced tools for document analysis, real-time file and web data integration, image understanding, and speech recognition. At the core of the platform lies a Retrieval Augmented Generation (<span>RAG</span>) framework, which improves the contextual relevance and factual accuracy of responses by incorporating external information sources. <span>Bio-Eng-LLM</span> also includes image generation via diffusion models and secure web-based search and summarization features. Its user-friendly interface supports multimodal interactions – text, image, and voice – enabling dynamic and personalized assistance in academic environments. By simplifying access to complex information and promoting interdisciplinary collaboration, <span>Bio-Eng-LLM</span> fosters <span>AI</span> literacy and facilitates both knowledge discovery and communication.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102260"},"PeriodicalIF":2.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655341","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}
SoftwareXPub Date : 2025-07-17DOI: 10.1016/j.softx.2025.102226
V. Kriukov, R. Rahman, L. Bastin
{"title":"Data4Land: How to enrich land-use/land-cover with historical vector(s)","authors":"V. Kriukov, R. Rahman, L. Bastin","doi":"10.1016/j.softx.2025.102226","DOIUrl":"10.1016/j.softx.2025.102226","url":null,"abstract":"<div><div>Land-use/land-cover (LULC) datasets produced from remote sensing may not consistently capture small/linear features of interest, including ecological barriers, eg. roads, railways and water objects. To overcome this challenge, a flexible workflow was developed to enrich the LULC with vector data (OpenStreetMap and World Database on Protected Areas). Users apply the Data4Land tool through a series of Jupyter Notebooks that address different mandatory and optional functions. The tool was used to enrich example LULC datasets and compute habitat connectivity indices for Catalonia (Spain) and Northern England. If vector data represent ecological barriers, connectivity indices tend to drop at all scales once the enriched LULC datasets are implemented.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102226"},"PeriodicalIF":2.4,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655340","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}
SoftwareXPub Date : 2025-07-16DOI: 10.1016/j.softx.2025.102265
Ana Waldila de Queiroz Ramiro Reis , Mayara Machado Martins , Rodrigo Bird Burgos
{"title":"Version 2.0 – “DYNAblast – A software to obtain the behavior of composite laminated plates subjected to blast loads”","authors":"Ana Waldila de Queiroz Ramiro Reis , Mayara Machado Martins , Rodrigo Bird Burgos","doi":"10.1016/j.softx.2025.102265","DOIUrl":"10.1016/j.softx.2025.102265","url":null,"abstract":"<div><div>New structural technologies are constantly being developed, especially in the case of high-impact loads, which cause significant demands on the structure's resistance to collapse. Thus, considering the evolution of material combination in the field of engineering, DYNAblast 2.0 software was developed, based on DYNAblast 1.1, to model and analyze composite orthotropic laminated plate structures when subjected to blast loads. For the software, several theories of laminated plates are applied, including the geometric non-linearity of the model.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102265"},"PeriodicalIF":2.4,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655342","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}
SoftwareXPub Date : 2025-07-15DOI: 10.1016/j.softx.2025.102252
Joseph Ramses Méndez Cam, Félix Melchor Santos López
{"title":"Inverse kinematics calculation in IEC 61131-3 Structured Text: KinIn","authors":"Joseph Ramses Méndez Cam, Félix Melchor Santos López","doi":"10.1016/j.softx.2025.102252","DOIUrl":"10.1016/j.softx.2025.102252","url":null,"abstract":"<div><div>IEC 61131-3 is a widely recognized standard in industrial programming, with its Structured Text programming language frequently employed for developing complex applications. However, there is a notable lack of comprehensive libraries for the analysis of custom mechanisms in Structured Text. To address the limitations associated with programming in IEC 61131-3, KinIn was developed as a framework implementing essential linear algebra operations and functions for inverse kinematics computation. This paper details the core components of the framework, the implemented functions, and their interconnections. The mathematical foundations of exponential coordinates used in the calculations are briefly introduced, and the framework’s utility is demonstrated through an illustrative example in the domain of heavy machinery.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102252"},"PeriodicalIF":2.4,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144632629","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}
SoftwareXPub Date : 2025-07-15DOI: 10.1016/j.softx.2025.102264
Logan Harbour , Guillaume Giudicelli , Alexander D. Lindsay , Peter German , Joshua Hansel , Casey Icenhour , Mengnan Li , Jason M. Miller , Roy H. Stogner , Patrick Behne , Daniel Yankura , Zachary M. Prince , Corey DeChant , Daniel Schwen , Benjamin W. Spencer , Mauricio Tano , Namjae Choi , Yaqi Wang , Max Nezdyur , Yinbin Miao , Cody J. Permann
{"title":"4.0 MOOSE: Enabling massively parallel Multiphysics simulation","authors":"Logan Harbour , Guillaume Giudicelli , Alexander D. Lindsay , Peter German , Joshua Hansel , Casey Icenhour , Mengnan Li , Jason M. Miller , Roy H. Stogner , Patrick Behne , Daniel Yankura , Zachary M. Prince , Corey DeChant , Daniel Schwen , Benjamin W. Spencer , Mauricio Tano , Namjae Choi , Yaqi Wang , Max Nezdyur , Yinbin Miao , Cody J. Permann","doi":"10.1016/j.softx.2025.102264","DOIUrl":"10.1016/j.softx.2025.102264","url":null,"abstract":"<div><div>Approaching 18 years of existence, MOOSE—the Multiphysics Object-Oriented Simulation Environment—is being developed at a higher pace than ever before. With significant support from four research institutions across the globe, and dozens of new contributors, the capabilities of the framework are being expanded to meet modeling challenges in a wide variety of fields from nuclear system design, to geomechanics, to material science. This includes new development in equation discretization techniques, solver methods, meshing capabilities, application deployment, and user interface improvements. Applications built on MOOSE benefit from all these improvements.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102264"},"PeriodicalIF":2.4,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144632631","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}
SoftwareXPub Date : 2025-07-15DOI: 10.1016/j.softx.2025.102270
Paweł Terefenko , Kamran Tanwari , Jakub Śledziowski , Andrzej Giza , Xiaohao Shi
{"title":"SCANDEM-Coast - open-source tool for UAV LiDAR point cloud classification in coastal environments","authors":"Paweł Terefenko , Kamran Tanwari , Jakub Śledziowski , Andrzej Giza , Xiaohao Shi","doi":"10.1016/j.softx.2025.102270","DOIUrl":"10.1016/j.softx.2025.102270","url":null,"abstract":"<div><div>Remote sensing technologies, particularly Light Detection and Ranging (LiDAR) mounted on Unnamed Aerial Vehicle (UAV), are instrumental in monitoring the dynamics of coastal environments. However, the utility of raw UAV LiDAR point clouds is often constrained by their unstructured format, lack of classification, presence of noise, and multiple returns, necessitating robust filtering algorithms. The complexity of pre-processing demands specialized expertise, and automated classification methods remain largely confined to specific research domains, limiting broader scientific application. To address these limitations, we developed the SCANDEM-Coast (SCanning and ANalysis for DEM generation in Morphodynamic Coastal environments) toolkit: a simplified, open-access, automated workflow for end-to-end processing of LiDAR datasets. It comprises of Python scripts, the toolkit streamlines the pre-processing, classification, interpolation and conversion of UAV LiDAR datasets to Digital Elevation Models (DEM) using well-developed algorithms and scientific methodologies to assess accuracy of produced DEMs.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"31 ","pages":"Article 102270"},"PeriodicalIF":2.4,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144632630","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}