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DEMLab: A Discrete Element Method development environment DEMLab：离散元素法开发环境
IF 2.1
Software Impacts Pub Date : 2024-06-06 DOI: 10.1016/j.simpa.2024.100670
Rafael L. Rangel
{"title":"DEMLab: A Discrete Element Method development environment","authors":"Rafael L. Rangel","doi":"10.1016/j.simpa.2024.100670","DOIUrl":"https://doi.org/10.1016/j.simpa.2024.100670","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000587/pdfft?md5=88fe948ace5e2f9bb4a1679c06706020&pid=1-s2.0-S2665963824000587-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141324664","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}
引用次数: 0
Python/NEURON code for simulating biophysically realistic thalamocortical dynamics during sleep 模拟睡眠期间丘脑皮层生物物理动态的 Python/NEURON 代码
IF 2.1
Software Impacts Pub Date : 2024-06-03 DOI: 10.1016/j.simpa.2024.100667
Christian G. Fink , Pavel Sanda , Logan Bayer , Eroma Abeysinghe , Maxim Bazhenov , Giri P. Krishnan
{"title":"Python/NEURON code for simulating biophysically realistic thalamocortical dynamics during sleep","authors":"Christian G. Fink ,&nbsp;Pavel Sanda ,&nbsp;Logan Bayer ,&nbsp;Eroma Abeysinghe ,&nbsp;Maxim Bazhenov ,&nbsp;Giri P. Krishnan","doi":"10.1016/j.simpa.2024.100667","DOIUrl":"10.1016/j.simpa.2024.100667","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000551/pdfft?md5=78ba384ded9e7d6f4cc71f0b1b5b31cf&pid=1-s2.0-S2665963824000551-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141274997","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}
引用次数: 0
BlockSupply: Blockchain-based logistics traceability solution BlockSupply：基于区块链的物流溯源解决方案
IF 2.1
Software Impacts Pub Date : 2024-05-27 DOI: 10.1016/j.simpa.2024.100666
Kamal Idrissi Zineb , Lachgar Mohamed , Hrimech Hamid , Yousfi Meryem , Layoune Ghita , Hanim Hanae
{"title":"BlockSupply: Blockchain-based logistics traceability solution","authors":"Kamal Idrissi Zineb ,&nbsp;Lachgar Mohamed ,&nbsp;Hrimech Hamid ,&nbsp;Yousfi Meryem ,&nbsp;Layoune Ghita ,&nbsp;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":null,"pages":null},"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}
引用次数: 0
GDPR Data Sharing Contract Management and Compliance Verification Tool GDPR 数据共享合同管理和合规性验证工具
IF 2.1
Software Impacts Pub Date : 2024-05-23 DOI: 10.1016/j.simpa.2024.100653
Amar Tauqeer , Anna Fensel
{"title":"GDPR Data Sharing Contract Management and Compliance Verification Tool","authors":"Amar Tauqeer ,&nbsp;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":null,"pages":null},"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}
引用次数: 0
LattGen: A TPMS lattice generation tool LattGen：TPMS 网格生成工具
IF 2.1
Software Impacts Pub Date : 2024-05-21 DOI: 10.1016/j.simpa.2024.100665
Hilda Chris-Amadin, Osezua Ibhadode
{"title":"LattGen: A TPMS lattice generation tool","authors":"Hilda Chris-Amadin,&nbsp;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":null,"pages":null},"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}
引用次数: 0
IDS-Anta: An open-source code with a defense mechanism to detect adversarial attacks for intrusion detection system IDS-Anta：带有防御机制的开源代码，用于检测入侵检测系统的对抗性攻击
IF 2.1
Software Impacts Pub Date : 2024-05-17 DOI: 10.1016/j.simpa.2024.100664
Kousik Barik , Sanjay Misra
{"title":"IDS-Anta: An open-source code with a defense mechanism to detect adversarial attacks for intrusion detection system","authors":"Kousik Barik ,&nbsp;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":null,"pages":null},"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}
引用次数: 0
Makita—A workflow generator for large-scale and reproducible simulation studies mimicking text labeling 牧田--模拟文本标注的大规模可重现模拟研究工作流程生成器
IF 2.1
Software Impacts Pub Date : 2024-05-17 DOI: 10.1016/j.simpa.2024.100663
Jelle Jasper Teijema , Rens van de Schoot , Gerbrich Ferdinands , Peter Lombaers , Jonathan de Bruin
{"title":"Makita—A workflow generator for large-scale and reproducible simulation studies mimicking text labeling","authors":"Jelle Jasper Teijema ,&nbsp;Rens van de Schoot ,&nbsp;Gerbrich Ferdinands ,&nbsp;Peter Lombaers ,&nbsp;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":null,"pages":null},"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}
引用次数: 0
R-code for calculating fluctuation assay results and 95% confidence intervals based on Ma–Sandri–Sarkar Maximum Likelihood 基于 Ma-Sandri-Sarkar 最大似然法计算波动检测结果和 95% 置信区间的 R 代码
IF 2.1
Software Impacts Pub Date : 2024-05-16 DOI: 10.1016/j.simpa.2024.100661
Ola Abdalla , Cameron Walker , Koichiro Ishimori
{"title":"R-code for calculating fluctuation assay results and 95% confidence intervals based on Ma–Sandri–Sarkar Maximum Likelihood","authors":"Ola Abdalla ,&nbsp;Cameron Walker ,&nbsp;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":null,"pages":null},"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}
引用次数: 0
The Munich Procedure – Standardising linear regression documentation in p-XRF research 慕尼黑程序--p-XRF 研究中线性回归文件的标准化
IF 2.1
Software Impacts Pub Date : 2024-05-14 DOI: 10.1016/j.simpa.2024.100660
Michaela Schauer , Frank Siegmund , Markus Helfert , Brandon Lee Drake
{"title":"The Munich Procedure – Standardising linear regression documentation in p-XRF research","authors":"Michaela Schauer ,&nbsp;Frank Siegmund ,&nbsp;Markus Helfert ,&nbsp;Brandon Lee Drake","doi":"10.1016/j.simpa.2024.100660","DOIUrl":"10.1016/j.simpa.2024.100660","url":null,"abstract":"<div><p>The Munich Procedure, a protocol presented as R code and initially developed on the basis of archaeometric portable X-ray fluorescence (p-XRF) data, offers adaptability and standardisation to evaluate coefficient corrections. These corrections are derived from linear regressions calculated by comparing p-XRF values with laboratory chemical analyses of the same sample set. The versatility of this procedure allows collaboration and ensures consistent data structure. Not tied to specific instrumentation, this approach helps to universally improve the accuracy of p-XRF data, benefiting specialists in a variety of industries. By providing a common baseline for performance evaluation, it enables discussion across different applications.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000484/pdfft?md5=29c4b19a13d58b415fbae2a6a4483d57&pid=1-s2.0-S2665963824000484-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141028352","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}
引用次数: 0
HELVES: A Python-based simulator to model circulation of electric vehicles on a highway HELVES：基于 Python 的模拟器，用于模拟电动汽车在高速公路上的通行情况
IF 2.1
Software Impacts Pub Date : 2024-05-11 DOI: 10.1016/j.simpa.2024.100658
Ekaterina Dudkina, Claudio Scarpelli
{"title":"HELVES: A Python-based simulator to model circulation of electric vehicles on a highway","authors":"Ekaterina Dudkina,&nbsp;Claudio Scarpelli","doi":"10.1016/j.simpa.2024.100658","DOIUrl":"10.1016/j.simpa.2024.100658","url":null,"abstract":"<div><p>Due to the stable increase in electric mobility, it is important to assess the growing burden on the power system in general and on the existing charging stations, to plan future development and extension of the electric infrastructure. The simulator proposed in this paper is based on Python software and allows modeling of the flow of electric vehicles circulating on a highway. It allows to evaluate the impact of electric vehicles for different penetration level, allocation strategies, charging rates and capacities of the charging stations. The simulator is applied to a case study to illustrate the functionalities of the code and a range of Key Performance Indicators is proposed to illustrate charging times. Finally, it is demonstrated that the simulator outcomes can highlight crucial aspects from both the drivers’ and the charging station operators’ perspectives.</p></div>","PeriodicalId":29771,"journal":{"name":"Software Impacts","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665963824000460/pdfft?md5=844b197a4d3dd5af8bc73c10975dd7bd&pid=1-s2.0-S2665963824000460-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141046985","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}
引用次数: 0
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