Pub Date : 2024-06-07DOI: 10.1016/j.simpa.2024.100668
Robert M. Auenhammer , Carolyn Oddy , Jisoo Kim , Lars P. Mikkelsen
For fibre-reinforced composites, most of their mechanical properties is tied to the fibre scale. Thus, imaging-based characterisation demands resolving fibres to characterise these materials accurately. However, high resolutions limit the field of view and lead to lengthy acquisition times. Emerging non-destructive imaging technologies and algorithms now accurately provide fibre orientations without detecting individual fibres. Studies show that voxel sizes up to fifteen times the fibre diameter are feasible, still allowing accurate tensile modulus predictions. Our presented software incorporates sub-voxel fibre orientation distributions using ultra-low-resolution three-dimensional X-ray tomography data in a numerical model, providing an effective method for characterising these materials.
对于纤维增强复合材料而言,其大部分机械特性都与纤维尺度有关。因此,基于成像的表征技术要求对纤维进行分辨,以准确表征这些材料。然而,高分辨率限制了视野,导致采集时间过长。现在,新兴的非破坏性成像技术和算法可以在不检测单个纤维的情况下准确提供纤维方向。研究表明,体素尺寸可达纤维直径的 15 倍是可行的,但仍能准确预测拉伸模量。我们介绍的软件将使用超低分辨三维 X 射线断层扫描数据的子体素纤维取向分布纳入数值模型中,为表征这些材料提供了一种有效的方法。
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Pub Date : 2024-06-07DOI: 10.1016/j.simpa.2024.100669
Benjamin Vignau, Patrice Clemente, Pascal Berthomé
This article describes a software suite designed for systematic and automatic literature reviews. Actually, we used these tools to help us build our systematic literature review on our research topic: biometric authentication using PPG (photoplethysmography). However, our tools can be easily applied (and have been applied) to other fields, whether scientific (state of the art) or technological (technology watch). Our software suite is made of two softwares. The first one helps to extract, merge and filter all the references in the pdf file versions of the papers. The second one helps to make statistical analysis on the dataset created for the SLR.
本文介绍了一套专为系统性自动文献综述而设计的软件。实际上,我们使用这些工具来帮助我们就我们的研究课题进行系统的文献综述:使用 PPG(血压计)进行生物识别。不过,我们的工具也可以很容易地应用于(而且已经应用于)其他领域,无论是科学领域(技术现状)还是技术领域(技术观察)。我们的软件套件由两个软件组成。第一个软件可帮助提取、合并和过滤论文 pdf 文件版本中的所有参考文献。第二个软件可对为 SLR 创建的数据集进行统计分析。
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Pub Date : 2024-06-06DOI: 10.1016/j.simpa.2024.100670
Rafael L. Rangel
Accurate multiphysics simulations of particle-formed materials are required in various engineering applications. The Discrete Element Method (DEM) stands out for its ability to capture the complex behavior of such materials. However, the multitude of particle interaction models and parameters involved pose challenges for analysts and researchers. DEMLab addresses this issue as an open-source MATLAB software that offers a user-friendly environment for exploring DEM models in small to medium-scale problems. With a modular and extensible code, it facilitates immediate implementations for testing different formulations or developing new ones. This paper details the software capabilities and how it impacts academic activities.
各种工程应用都需要对颗粒成型材料进行精确的多物理场模拟。离散元素法(DEM)因其能够捕捉此类材料的复杂行为而脱颖而出。然而,大量的颗粒相互作用模型和参数给分析人员和研究人员带来了挑战。DEMLab 解决了这一问题,它是一款开源的 MATLAB 软件,为探索中小型问题中的 DEM 模型提供了用户友好型环境。该软件采用模块化和可扩展的代码,便于立即实施,以测试不同的计算公式或开发新的计算公式。本文将详细介绍该软件的功能及其对学术活动的影响。
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Pub Date : 2024-06-03DOI: 10.1016/j.simpa.2024.100667
Christian G. Fink , Pavel Sanda , Logan Bayer , Eroma Abeysinghe , Maxim Bazhenov , Giri P. Krishnan
Understanding the function of sleep and its associated neural rhythms is an important goal in neuroscience. While many theoretical models of neural dynamics during sleep exist, few include the effects of neuromodulators on sleep oscillations and describe transitions between sleep and wake states or different sleep stages. Here, we started with a C++-based thalamocortical network model that describes characteristic thalamic and cortical oscillations specific to sleep. This model, which includes a biophysically realistic description of intrinsic and synaptic channels, allows for testing the effects of different neuromodulators, intrinsic cell properties, and synaptic connectivity on neural dynamics during sleep. We present a complete reimplementation of this previously-published sleep model in the standardized NEURON/Python framework, making it more accessible to the wider scientific community.
了解睡眠及其相关神经节律的功能是神经科学的一个重要目标。虽然已有许多睡眠期间神经动态的理论模型,但很少有模型包括神经调节剂对睡眠振荡的影响,以及睡眠和觉醒状态或不同睡眠阶段之间的转换。在这里,我们从一个基于 C++ 的丘脑皮层网络模型入手,该模型描述了睡眠特有的丘脑和皮层振荡特征。该模型包括对内在和突触通道的生物物理现实描述,可用于测试不同神经调节剂、细胞内在特性和突触连接对睡眠期间神经动力学的影响。我们在标准化的 NEURON/Python 框架中重新完整地实现了这一以前发表的睡眠模型,使其更容易为更广泛的科学界所使用。
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The BlockSupply project is a pioneering initiative that seeks to redefine supply chain management by leveraging blockchain technology to ensure real-time monitoring of product movements and enhance transparency, security, and traceability. The software offers key functionalities such as creating a private blockchain network, integrating tracking sensors for real-time data collection, secure recording of product data, user authentication, authorization management, and alerts for abnormal events. It is developed using technologies like Web3.js, React.js, Solidity, Ganache, and GitHub, which are integrated into the project’s architecture to create an efficient and secure blockchain-based supply chain solution. Furthermore, the project’s impact is expected to be significant, contributing to scientific advancements in secure and efficient supply chain operations and reshaping the landscape of logistics traceability. As the software gains traction in real-world scenarios, its transformative influence on data reliability, security, and operational efficiency in supply chain research is poised to be showcased in publications.
{"title":"BlockSupply: Blockchain-based logistics traceability solution","authors":"Kamal Idrissi Zineb , Lachgar Mohamed , Hrimech Hamid , Yousfi Meryem , Layoune Ghita , Hanim Hanae","doi":"10.1016/j.simpa.2024.100666","DOIUrl":"https://doi.org/10.1016/j.simpa.2024.100666","url":null,"abstract":"<div><p>The BlockSupply project is a pioneering initiative that seeks to redefine supply chain management by leveraging blockchain technology to ensure real-time monitoring of product movements and enhance transparency, security, and traceability. The software offers key functionalities such as creating a private blockchain network, integrating tracking sensors for real-time data collection, secure recording of product data, user authentication, authorization management, and alerts for abnormal events. It is developed using technologies like Web3.js, React.js, Solidity, Ganache, and GitHub, which are integrated into the project’s architecture to create an efficient and secure blockchain-based supply chain solution. Furthermore, the project’s impact is expected to be significant, contributing to scientific advancements in secure and efficient supply chain operations and reshaping the landscape of logistics traceability. As the software gains traction in real-world scenarios, its transformative influence on data reliability, security, and operational efficiency in supply chain research is poised to be showcased in publications.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100666"},"PeriodicalIF":2.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S266596382400054X/pdfft?md5=ba5dbadbce6d28394478120e237f4386&pid=1-s2.0-S266596382400054X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141241625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-23DOI: 10.1016/j.simpa.2024.100653
Amar Tauqeer , Anna Fensel
General Data Protection Regulation (GDPR) is compulsory for processing personally identifiable data (PID) across Europe after 2018. Specifically when sharing research data, we cannot process PID without a legal basis defined by GDPR. To facilitate this, we present a scalable and interoperable automated Contract Compliance Verification (CCV) tool that enables GDPR-compliant contract management and data sharing. With the implementation of two scenarios in smart cities and insurance domains, we show how CCV is helpful to process PID and make data collection and integration (e.g., from crowdsourcing) easier.
{"title":"GDPR Data Sharing Contract Management and Compliance Verification Tool","authors":"Amar Tauqeer , Anna Fensel","doi":"10.1016/j.simpa.2024.100653","DOIUrl":"10.1016/j.simpa.2024.100653","url":null,"abstract":"<div><p>General Data Protection Regulation (GDPR) is compulsory for processing personally identifiable data (PID) across Europe after 2018. Specifically when sharing research data, we cannot process PID without a legal basis defined by GDPR. To facilitate this, we present a scalable and interoperable automated Contract Compliance Verification (CCV) tool that enables GDPR-compliant contract management and data sharing. With the implementation of two scenarios in smart cities and insurance domains, we show how CCV is helpful to process PID and make data collection and integration (<em>e.g.</em>, from crowdsourcing) easier.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100653"},"PeriodicalIF":2.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000411/pdfft?md5=40bfb412e501656e51d9fd42b6f84fe8&pid=1-s2.0-S2665963824000411-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141138202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-21DOI: 10.1016/j.simpa.2024.100665
Hilda Chris-Amadin, Osezua Ibhadode
Triply Periodic Minimal Surfaces (TPMS) are parametrically generated lattices with topology-driven properties. They are emerging as a significant innovation, finding wide-ranging applications. This paper introduces LattGen, a software solution that addresses the complexity of designing these surfaces. This tool allows users to easily customize their desired surfaces’ size, volume fraction, grading, and hybridization. LattGen also allows for the import of arbitrary domains and the export to standard computer-aided design platforms for additive manufacturing. This design platform automates the creation of porous structures, making them a valuable tool in various scientific, engineering, and creative fields.
{"title":"LattGen: A TPMS lattice generation tool","authors":"Hilda Chris-Amadin, Osezua Ibhadode","doi":"10.1016/j.simpa.2024.100665","DOIUrl":"10.1016/j.simpa.2024.100665","url":null,"abstract":"<div><p>Triply Periodic Minimal Surfaces (TPMS) are parametrically generated lattices with topology-driven properties. They are emerging as a significant innovation, finding wide-ranging applications. This paper introduces LattGen, a software solution that addresses the complexity of designing these surfaces. This tool allows users to easily customize their desired surfaces’ size, volume fraction, grading, and hybridization. LattGen also allows for the import of arbitrary domains and the export to standard computer-aided design platforms for additive manufacturing. This design platform automates the creation of porous structures, making them a valuable tool in various scientific, engineering, and creative fields.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100665"},"PeriodicalIF":2.1,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000538/pdfft?md5=32f6b64df9a901faca173be65d71d958&pid=1-s2.0-S2665963824000538-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141145608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-17DOI: 10.1016/j.simpa.2024.100664
Kousik Barik , Sanjay Misra
An intrusion detection system (IDS) is critical in protecting organizations from cyber threats. The susceptibility of Machine Learning and Deep Learning-based IDSs against adversarial attacks arises from malicious actors’ deliberate construction of adversarial samples. This study proposes a Python-based open-source code repository named IDS-Anta with a robust defense mechanism to identify adversarial attacks without compromising IDS performance. It uses Multi-Armed Bandits with Thomson Sampling, Ant Colony Optimization (ACO), and adversarial attack generation methods and is validated using three public benchmark datasets. This code repository can be readily applied and replicated on IDS datasets against adversarial attacks.
{"title":"IDS-Anta: An open-source code with a defense mechanism to detect adversarial attacks for intrusion detection system","authors":"Kousik Barik , Sanjay Misra","doi":"10.1016/j.simpa.2024.100664","DOIUrl":"10.1016/j.simpa.2024.100664","url":null,"abstract":"<div><p>An intrusion detection system (IDS) is critical in protecting organizations from cyber threats. The susceptibility of Machine Learning and Deep Learning-based IDSs against adversarial attacks arises from malicious actors’ deliberate construction of adversarial samples. This study proposes a Python-based open-source code repository named IDS-Anta with a robust defense mechanism to identify adversarial attacks without compromising IDS performance. It uses Multi-Armed Bandits with Thomson Sampling, Ant Colony Optimization (ACO), and adversarial attack generation methods and is validated using three public benchmark datasets. This code repository can be readily applied and replicated on IDS datasets against adversarial attacks.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100664"},"PeriodicalIF":2.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000526/pdfft?md5=aacd52378832dbdb16f9a40062336eeb&pid=1-s2.0-S2665963824000526-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141054145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-17DOI: 10.1016/j.simpa.2024.100663
Jelle Jasper Teijema , Rens van de Schoot , Gerbrich Ferdinands , Peter Lombaers , Jonathan de Bruin
This paper introduces ASReview Makita, a tool designed to enhance the efficiency and reproducibility of simulation studies in systematic reviews. Makita streamlines the setup of large-scale simulation studies by automating workflow generation, repository preparation, and script execution. It employs Jinja and Python templates to create a structured, reproducible environment, aiding both novice and expert researchers. Makita’s flexibility allows for customization to specific research needs, ensuring a repeatable research process. This tool represents an advancement in the field of systematic review automation, offering a practical solution to the challenges of managing complex simulation studies.
{"title":"Makita—A workflow generator for large-scale and reproducible simulation studies mimicking text labeling","authors":"Jelle Jasper Teijema , Rens van de Schoot , Gerbrich Ferdinands , Peter Lombaers , Jonathan de Bruin","doi":"10.1016/j.simpa.2024.100663","DOIUrl":"10.1016/j.simpa.2024.100663","url":null,"abstract":"<div><p>This paper introduces ASReview Makita, a tool designed to enhance the efficiency and reproducibility of simulation studies in systematic reviews. Makita streamlines the setup of large-scale simulation studies by automating workflow generation, repository preparation, and script execution. It employs Jinja and Python templates to create a structured, reproducible environment, aiding both novice and expert researchers. Makita’s flexibility allows for customization to specific research needs, ensuring a repeatable research process. This tool represents an advancement in the field of systematic review automation, offering a practical solution to the challenges of managing complex simulation studies.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100663"},"PeriodicalIF":2.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000514/pdfft?md5=c9ac8c4c6f21f6c1c0ac0aaf6d975b7f&pid=1-s2.0-S2665963824000514-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141045170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-16DOI: 10.1016/j.simpa.2024.100661
Ola Abdalla , Cameron Walker , Koichiro Ishimori
The Luria–Delbrück fluctuation assay is an essential experiment in calculating mutation rates, especially in genetic and mutation research. Its reliability and accuracy have made it the go-to method for numerous researchers. In this article, we provide an R-code that statistically analyzes the assay results more easily and offers the most challenging code for calculating 95% confidence intervals based on the gold standard method “Ma–Sandri–Sarkar Maximum Likelihood.” Recently, the maximization of the likelihood function through optimization functions in R can be a challenging task. The recursive format of the likelihood function is known to cause memory stack issues. Our findings indicate that utilizing a non-recursive version of the function can increase the tractability of the maximization process. With this code, future scientists can unlock valuable statistical insights related to the biological mechanisms that drive genetic variation and can, therefore, contribute to developing novel therapeutic interventions and innovative solutions to various biological and medical challenges.
卢里亚-德尔布吕克波动测定法是计算突变率的重要实验,尤其是在遗传和突变研究中。它的可靠性和准确性使其成为众多研究人员的首选方法。在这篇文章中,我们提供了一个 R 代码,可以更轻松地对测定结果进行统计分析,并提供了基于黄金标准方法 "Ma-Sandri-Sarkar 最大似然法" 计算 95% 置信区间的最具挑战性的代码。最近,通过 R 中的优化函数最大化似然函数是一项具有挑战性的任务。众所周知,似然函数的递归格式会导致内存堆栈问题。我们的研究结果表明,利用该函数的非递归版本可以提高最大化过程的可操作性。有了这套代码,未来的科学家就能获得与驱动遗传变异的生物机制有关的宝贵统计见解,从而有助于开发新型治疗干预措施和创新解决方案,应对各种生物和医学挑战。
{"title":"R-code for calculating fluctuation assay results and 95% confidence intervals based on Ma–Sandri–Sarkar Maximum Likelihood","authors":"Ola Abdalla , Cameron Walker , Koichiro Ishimori","doi":"10.1016/j.simpa.2024.100661","DOIUrl":"10.1016/j.simpa.2024.100661","url":null,"abstract":"<div><p>The Luria–Delbrück fluctuation assay is an essential experiment in calculating mutation rates, especially in genetic and mutation research. Its reliability and accuracy have made it the go-to method for numerous researchers. In this article, we provide an R-code that statistically analyzes the assay results more easily and offers the most challenging code for calculating 95% confidence intervals based on the gold standard method “Ma–Sandri–Sarkar Maximum Likelihood.” Recently, the maximization of the likelihood function through optimization functions in R can be a challenging task. The recursive format of the likelihood function is known to cause memory stack issues. Our findings indicate that utilizing a non-recursive version of the function can increase the tractability of the maximization process. With this code, future scientists can unlock valuable statistical insights related to the biological mechanisms that drive genetic variation and can, therefore, contribute to developing novel therapeutic interventions and innovative solutions to various biological and medical challenges.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":"21 ","pages":"Article 100661"},"PeriodicalIF":2.1,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000496/pdfft?md5=194bbb520b843fb425f09fd1806a704f&pid=1-s2.0-S2665963824000496-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141027441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}