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smFISH_batchRun: A smFISH image processing tool for single-molecule RNA Detection and 3D reconstruction smFISH_batchRun：用于单分子RNA检测和3D重建的smFISH图像处理工具
IF 1.3
Software Impacts Pub Date : 2025-07-01 DOI: 10.1016/j.simpa.2025.100777
Nimmy S. John, ChangHwan Lee
{"title":"smFISH_batchRun: A smFISH image processing tool for single-molecule RNA Detection and 3D reconstruction","authors":"Nimmy S. John,&nbsp;ChangHwan Lee","doi":"10.1016/j.simpa.2025.100777","DOIUrl":"10.1016/j.simpa.2025.100777","url":null,"abstract":"<div><div>Single-molecule RNA imaging has been made possible with the recent advances in microscopy methods. However, systematic analysis of these images has been challenging due to the highly variable background noise, even after applying sophisticated computational clearing methods. Here, we describe our custom MATLAB scripts that allow us to detect both nuclear nascent transcripts at the active transcription sites (ATS) and mature cytoplasmic mRNAs with single-molecule precision and reconstruct the tissue in 3D for further analysis. Our codes were initially optimized for the <em>C. elegans</em> germline but were designed to be broadly applicable to other species and tissue types.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100777"},"PeriodicalIF":1.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144595977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EVRPGen: A web-based instance generator for the electric vehicle routing problem with road junctions and road types EVRPGen：一个基于网络的实例生成器，用于解决具有道路交叉点和道路类型的电动汽车路线问题
IF 1.3
Software Impacts Pub Date : 2025-07-01 DOI: 10.1016/j.simpa.2025.100778
Mehmet Anil Akbay , Christian Blum
{"title":"EVRPGen: A web-based instance generator for the electric vehicle routing problem with road junctions and road types","authors":"Mehmet Anil Akbay ,&nbsp;Christian Blum","doi":"10.1016/j.simpa.2025.100778","DOIUrl":"10.1016/j.simpa.2025.100778","url":null,"abstract":"<div><div>This paper presents a web-based instance generator for Electric Vehicle Routing Problems (EVRP) with Road Junctions and Road Types, using OpenStreetMap data. Users define an area, specify network components (depots, customers, charging stations, junctions), and customize vehicle parameters. The React-based frontend enables configuration, visualization, and queries, while the Flask backend processes road networks, classifies road types, and assigns demand and service times. A RESTful API ensures real-time instance generation. Generated instances can be downloaded as text-based datasets and interactive visualizations. The tool is open-source and contributes to the area of sustainable transportation by enabling scenario-based EVRP experimentation.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100778"},"PeriodicalIF":1.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144549445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TR-VABML: Enhancing Turkish vocabulary acquisition through adaptive machine learning classification TR-VABML：通过自适应机器学习分类增强土耳其语词汇习得
IF 1.3
Software Impacts Pub Date : 2025-06-17 DOI: 10.1016/j.simpa.2025.100774
Ahmed Alaff , Çelebi Uluyol
{"title":"TR-VABML: Enhancing Turkish vocabulary acquisition through adaptive machine learning classification","authors":"Ahmed Alaff ,&nbsp;Çelebi Uluyol","doi":"10.1016/j.simpa.2025.100774","DOIUrl":"10.1016/j.simpa.2025.100774","url":null,"abstract":"<div><div>Conventional vocabulary assessments emphasize precision rather than hesitation and rapidity. A machine learning system was developed utilizing behavioral analysis and linguistic insights to identify vocabulary gaps in Turkish language learners. This system integrates hesitation counts, reaction times, and answer attempts with word difficulty and thematic elements. Vocabulary strength was computed using a rule-based equation derived from behavioral indications. With 89% accuracy, 86% precision, 91% recall, and an 88% F1 score, the model showed better performance than the linear and Poisson kernel alternatives. By effectively separating complex interactions, the RBF kernel minimizes unnecessary actions and ensures accurate identification of real shortages.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100774"},"PeriodicalIF":1.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144313054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nyctophy: Development of virtual reality and smartwatch integrated serious game for nyctophobia therapy 夜游：开发虚拟现实与智能手表相结合的夜游恐惧症治疗严肃游戏
IF 1.3
Software Impacts Pub Date : 2025-06-14 DOI: 10.1016/j.simpa.2025.100770
Dimas Ramdhan, Elshad Ryan Ardiyanto, Patrick Alexander, Edyth Novian Putra, David
{"title":"Nyctophy: Development of virtual reality and smartwatch integrated serious game for nyctophobia therapy","authors":"Dimas Ramdhan,&nbsp;Elshad Ryan Ardiyanto,&nbsp;Patrick Alexander,&nbsp;Edyth Novian Putra,&nbsp;David","doi":"10.1016/j.simpa.2025.100770","DOIUrl":"10.1016/j.simpa.2025.100770","url":null,"abstract":"<div><div>Nyctophy is a serious game combining virtual reality (VR) and smartwatch integration for nyctophobia (fear of darkness) therapy. The paper thoroughly explores its development framework, simulating dark environments with real-time heart rate monitoring and adaptive flashlight mechanics. Built in Unity Engine, Nyctophy supports VR (Meta Quest 2) and keyboard–mouse interfaces. Performance tests achieved 71.9 FPS (”good” quality) across four devices. Tests with 34 participants revealed longer VR completion times (8:12 min) versus keyboard–mouse (3:54), highlighting immersive impact. Nyctophy demonstrates potential as a safe, innovative tool for diagnosing and treating nyctophobia, leveraging serious games to enhance accessibility and therapeutic outcomes.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100770"},"PeriodicalIF":1.3,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TERANG: Seismic loss estimation tool for school buildings TERANG：学校建筑地震损失估算工具
IF 1.3
Software Impacts Pub Date : 2025-06-10 DOI: 10.1016/j.simpa.2025.100773
Roi Milyardi , Krishna Suryanto Pribadi , Muhamad Abduh , Irwan Meilano , Erwin Lim
{"title":"TERANG: Seismic loss estimation tool for school buildings","authors":"Roi Milyardi ,&nbsp;Krishna Suryanto Pribadi ,&nbsp;Muhamad Abduh ,&nbsp;Irwan Meilano ,&nbsp;Erwin Lim","doi":"10.1016/j.simpa.2025.100773","DOIUrl":"10.1016/j.simpa.2025.100773","url":null,"abstract":"<div><div>This article presents a MATLAB-based computational software, TERANG to estimate physical and operational losses for school building in Indonesia. The basis of the estimation model used is the HAZUS model. TERANG provides modifications to the HAZUS model on school building cost parameters and reconstruction cost, as well as adjustments to local hazard data. TERANG provides an overview of the HAZUS model adoption process for countries that do not yet have a school building database. TERANG software supports Indonesia’s seismic loss studies, estimating school damages in Bandung and Mamuju’s 2021 earthquake while raising awareness among school stakeholders.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100773"},"PeriodicalIF":1.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144313009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MRI-based Alzheimer’s disease classification using Vision Transformer and time-series transformer: A step-by-step guide 基于mri的阿尔茨海默病分类使用视觉变压器和时间序列变压器：一步一步的指南
IF 1.3
Software Impacts Pub Date : 2025-06-10 DOI: 10.1016/j.simpa.2025.100771
Sait Alp , Sara Akan , Taymaz Akan , Mohammad Alfrad Nobel Bhuiyan
{"title":"MRI-based Alzheimer’s disease classification using Vision Transformer and time-series transformer: A step-by-step guide","authors":"Sait Alp ,&nbsp;Sara Akan ,&nbsp;Taymaz Akan ,&nbsp;Mohammad Alfrad Nobel Bhuiyan","doi":"10.1016/j.simpa.2025.100771","DOIUrl":"10.1016/j.simpa.2025.100771","url":null,"abstract":"<div><div>This study introduces a reproducible pipeline for classifying Alzheimer’s Disease from structural brain MRI utilizing a joint transformer architecture that integrates Vision Transformer and Time-Series Transformer models. The proposed framework uses pre-trained ViT for feature extraction from 2D slices of MRI volumes, followed by sequential modeling with a transformer-based classifier to capture inter-slice dependencies. The method is evaluated on the ADNI dataset, involving both binary (AD vs. NC) and multiclass (AD, MCI, NC) classification tasks across axial, sagittal, and coronal planes.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100771"},"PeriodicalIF":1.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144298005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
GD4Shapes: Geodesic distance with fixed parameterization for 2D Shapes GD4Shapes: 2D形状的固定参数化测地线距离
IF 1.3
Software Impacts Pub Date : 2025-06-10 DOI: 10.1016/j.simpa.2025.100775
S. Herold-Garcia , H.L. Varona-Gonzalez , X. Gual-Arnau
{"title":"GD4Shapes: Geodesic distance with fixed parameterization for 2D Shapes","authors":"S. Herold-Garcia ,&nbsp;H.L. Varona-Gonzalez ,&nbsp;X. Gual-Arnau","doi":"10.1016/j.simpa.2025.100775","DOIUrl":"10.1016/j.simpa.2025.100775","url":null,"abstract":"<div><div>Shape analysis within shape space provides a robust framework for examining geometric properties of objects, enabling comparisons invariant to translation, rotation, and scaling. A key task is computing geodesic distances between shapes, which quantify similarity but are computationally intensive due to the need for exhaustive parameterization searches. Recent advancements propose heuristic methods to simplify these computations, such as fixing parameterizations based on the major axis of shapes, significantly reducing computational costs while maintaining high accuracy (e.g., 96.03% in erythrocyte classification). This article introduces a software tool that leverages this heuristic to efficiently compute shape-space distances, aligning shapes considering their major axis, and using templates like circles and ellipses. The tool accelerates morphological analysis, making it ideal for high performance applications in fields like biology and medicine. By streamlining the computation of geodesic distances between shapes and enabling rapid retrieval of information, this software improves research workflows and supports the study of shape-dependent features in diverse fields from cellular morphology to diagnostic hematology.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100775"},"PeriodicalIF":1.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144313053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ESCOX: A tool for skill and occupation extraction using LLMs from unstructured text ESCOX：一个使用llm从非结构化文本中提取技能和职业的工具
IF 1.3
Software Impacts Pub Date : 2025-06-10 DOI: 10.1016/j.simpa.2025.100772
Dimitrios Christos Kavargyris , Konstantinos Georgiou , Eleanna Papaioannou , Konstantinos Petrakis , Nikolaos Mittas , Lefteris Angelis
{"title":"ESCOX: A tool for skill and occupation extraction using LLMs from unstructured text","authors":"Dimitrios Christos Kavargyris ,&nbsp;Konstantinos Georgiou ,&nbsp;Eleanna Papaioannou ,&nbsp;Konstantinos Petrakis ,&nbsp;Nikolaos Mittas ,&nbsp;Lefteris Angelis","doi":"10.1016/j.simpa.2025.100772","DOIUrl":"10.1016/j.simpa.2025.100772","url":null,"abstract":"<div><div>ESCOX, also known as ESCOSkillExtractor, is an open-source, non-proprietary tool for identifying and classifying skills, skillsets, and occupations from job postings and general text. It utilizes the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy to structure extraction, addressing the need for taxonomy-aligned skill identification in unstructured labor market data. Developed within the SKILLAB EU Horizon project, ESCOX combines LLMs and text embeddings to map content to standardized categories. It offers a user-friendly graphical interface for researchers, educators, and HR professionals, supporting skills gap analysis, training, recruitment, and policy planning, and contributing to the development of a skills-based economy.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100772"},"PeriodicalIF":1.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144263644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A practical open-source approach to Model Predictive Control using the Legendre–Gauss–Radau pseudospectral method 一个实用的开源方法模型预测控制使用legende - gauss - radau伪谱方法
IF 1.3
Software Impacts Pub Date : 2025-05-22 DOI: 10.1016/j.simpa.2025.100769
Saeid Bayat, James T. Allison
{"title":"A practical open-source approach to Model Predictive Control using the Legendre–Gauss–Radau pseudospectral method","authors":"Saeid Bayat,&nbsp;James T. Allison","doi":"10.1016/j.simpa.2025.100769","DOIUrl":"10.1016/j.simpa.2025.100769","url":null,"abstract":"<div><div>In a world increasingly reliant on technologies that sense and respond to their environment – from thermostats to energy grids – predictive capabilities are critical. However, uncertainties and complexity often hinder the adoption of advanced strategies like Model Predictive Control (MPC), leading many industries to rely on simpler, less effective methods. This paper presents a practical, open-source software tool based on the Legendre–Gauss–Radau pseudospectral method, designed to streamline MPC implementation. The software handles dynamics, constraints, and objectives efficiently while supporting black-box systems. A case study in this paper demonstrates its effectiveness, with additional examples in the supplementary material validating its versatility.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100769"},"PeriodicalIF":1.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reconstructing software evolution: Traceability from code commits to fault manifestation in CI 重构软件演化：从代码提交到CI中的错误表现的可追溯性
IF 1.3
Software Impacts Pub Date : 2025-05-19 DOI: 10.1016/j.simpa.2025.100767
Azeem Ahmad , Muhammad Rashid Naeem , Yasir Javed , Mohammad Akour
{"title":"Reconstructing software evolution: Traceability from code commits to fault manifestation in CI","authors":"Azeem Ahmad ,&nbsp;Muhammad Rashid Naeem ,&nbsp;Yasir Javed ,&nbsp;Mohammad Akour","doi":"10.1016/j.simpa.2025.100767","DOIUrl":"10.1016/j.simpa.2025.100767","url":null,"abstract":"<div><div>This paper presents <em>Eiffel-Store</em>, an open-source tool for real-time traceability in Continuous Integration (CI) pipelines. Unlike traditional batch visualization tools, Eiffel-Store dynamically visualizes live Eiffel events from CI tools (e.g., Jenkins) using MongoDB and Meteor.js. It supports incremental updates, enabling users to trace faults back to specific commits across the pipeline. Events can be streamed from RabbitMQ or added manually, offering flexibility for diverse workflows. By connecting code changes to final product faults, Eiffel-Store improves transparency, debugging, and quality assurance. The tool has been tested with industry partners and is available publicly to promote adoption and further development.</div></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"25 ","pages":"Article 100767"},"PeriodicalIF":1.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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