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Spora : a journal of biomathematics最新文献

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Web Application for Simulation of an Agent-Based Model in NetLogo3D. NetLogo3D中基于agent模型仿真的Web应用。
Spora : a journal of biomathematics Pub Date : 2025-01-01 Epub Date: 2025-03-27 DOI: 10.61403/2473-5493.1107
Chris Davis Perumal, Abraham Nofal, Benedict J Kolber, Rachael Miller Neilan
{"title":"Web Application for Simulation of an Agent-Based Model in NetLogo3D.","authors":"Chris Davis Perumal, Abraham Nofal, Benedict J Kolber, Rachael Miller Neilan","doi":"10.61403/2473-5493.1107","DOIUrl":"10.61403/2473-5493.1107","url":null,"abstract":"<p><p>Agent-based models (ABMs) are computer simulation models for studying systems of autonomous agents. Modelers often use specialized software like NetLogo to develop ABMs, but this software poses barriers to researchers in other disciplines with no prior programming experience. To address this issue, we developed a web application that allows users to simulate our ABM via a web browser, eliminating the need for the user to download and use specialized software. While presented in the context of a specific ABM, our approach can be applied to other ABMs to enhance accessibility. The ABM presented here was developed in NetLogo3D. The model simulates pain-related neural activity in the central nucleus of the amygdala and generates an emergent measure of pain output. The web application enables users to modify parameters, run simulations, visualize output, and export data without interacting with the model's code or downloading software, broadening access to researchers and the public.</p>","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"11 1","pages":"64-75"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12199284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509923","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
Improved Efficiency and Sensitivity Analysis of 3-D Agent-based Model for Pain-related Neural Activity in the Amygdala. 基于三维代理的杏仁核疼痛相关神经活动模型的效率和灵敏度分析的改进
Spora : a journal of biomathematics Pub Date : 2024-01-01 Epub Date: 2024-07-01 DOI: 10.61403/2473-5493.1094
Kayla Kraeuter, Carley Reith, Benedict J Kolber, Rachael Miller Neilan
{"title":"Improved Efficiency and Sensitivity Analysis of 3-D Agent-based Model for Pain-related Neural Activity in the Amygdala.","authors":"Kayla Kraeuter, Carley Reith, Benedict J Kolber, Rachael Miller Neilan","doi":"10.61403/2473-5493.1094","DOIUrl":"10.61403/2473-5493.1094","url":null,"abstract":"<p><p>Neuropathic pain is caused by nerve injury and involves brain areas such as the central nucleus of the amygdala (CeA). We developed the first 3-D agent-based model (ABM) of neuropathic pain-related neurons in the CeA using NetLogo3D. The execution time of a single ABM simulation using realistic parameters (e.g., 13,000 neurons and 22,000+ neural connections) is an important factor in the model's usability. In this paper, we describe our efforts to improve the computational efficiency of our 3-D ABM, which resulted in a 28% reduction in execution time on average for a typical simulation. With this upgraded model, we performed one- and two-parameter sensitivity analyses to study the sensitivity of model output to variability in several key parameters along the anterior to posterior axis of the CeA. These results highlight the importance of computational modeling in exploring spatial and cell-type specific properties of brain regions to inform future wet lab experiments.</p>","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"10 1","pages":"65-82"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11243734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617779","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
An Investigation of Mitigation Measures on the Spread of COVID-19 in a College Classroom Using Agent-Based Modeling 基于agent模型的高校课堂防控措施研究
Spora : a journal of biomathematics Pub Date : 2023-10-25 DOI: 10.61403/2473-5493.1086
Saharsh Talwar, Anne E Yust
{"title":"An Investigation of Mitigation Measures on the Spread of COVID-19 in a College Classroom Using Agent-Based Modeling","authors":"Saharsh Talwar, Anne E Yust","doi":"10.61403/2473-5493.1086","DOIUrl":"https://doi.org/10.61403/2473-5493.1086","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"23 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135168285","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
Bright Days Ahead 光明的未来
Spora : a journal of biomathematics Pub Date : 2023-01-01 DOI: 10.30707/spora9.1.1675492827.518619
{"title":"Bright Days Ahead","authors":"","doi":"10.30707/spora9.1.1675492827.518619","DOIUrl":"https://doi.org/10.30707/spora9.1.1675492827.518619","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73403846","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 Statistical Analysis of the Change in Age Distribution of Spawning Hatchery Salmon 孵化场鲑鱼产卵年龄分布变化的统计分析
Spora : a journal of biomathematics Pub Date : 2023-01-01 DOI: 10.30707/spora9.1.1675492827.538909
Rachel Macaulay, E. Barrett, Grace Penunuri, Eli E. Goldwyn
{"title":"A Statistical Analysis of the Change in Age Distribution of Spawning Hatchery Salmon","authors":"Rachel Macaulay, E. Barrett, Grace Penunuri, Eli E. Goldwyn","doi":"10.30707/spora9.1.1675492827.538909","DOIUrl":"https://doi.org/10.30707/spora9.1.1675492827.538909","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84110527","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
Effects of Disturbance and Conspecific Negative Density Dependence on Forest Composition and Diversity: A Simulation-Based Approach 干扰和同种负密度依赖对森林组成和多样性的影响:基于模拟的方法
Spora : a journal of biomathematics Pub Date : 2023-01-01 DOI: 10.30707/spora9.1.1680320335.532081
M. Mills, D. M. Chan, Benjamin S Ramage
{"title":"Effects of Disturbance and Conspecific Negative Density Dependence on Forest Composition and Diversity: A Simulation-Based Approach","authors":"M. Mills, D. M. Chan, Benjamin S Ramage","doi":"10.30707/spora9.1.1680320335.532081","DOIUrl":"https://doi.org/10.30707/spora9.1.1680320335.532081","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"124 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89417442","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
Modeling the Population Demographics & Viability of Imperiled Guzmania monostachia Populations 濒危古兹马种群的人口统计学和生存能力建模
Spora : a journal of biomathematics Pub Date : 2023-01-01 DOI: 10.30707/spora9.1.1690388424.437952
H. Pennington, Pranay Lingareddy, Erin N. Bodine
{"title":"Modeling the Population Demographics & Viability of Imperiled Guzmania monostachia Populations","authors":"H. Pennington, Pranay Lingareddy, Erin N. Bodine","doi":"10.30707/spora9.1.1690388424.437952","DOIUrl":"https://doi.org/10.30707/spora9.1.1690388424.437952","url":null,"abstract":"Guzmania monostachia is a large, long-lived bromeliad whose leaves grow in a rosette pattern and is native to the Americas, but endangered in Florida due to damage caused by the invasive weevil Metamasius callizona. Each G. monostachia rosette can reproduce sexually via flowers or asexually by producing clonal offshoot rosettes. We model the population dynamics and demographic structure of a G. monostachia population using a Lefkovitch matrix model where each state represents a demographic class of rosettes. Model analysis over a range of uncertain parameters show the conditions under which a G. monostachia population is viable in the absence and presence of M. callizona, and the expected demographic structure under those conditions. In particular, our analysis illustrates that proportional reductions in survival have a qualitatively stronger impact on population viability than proportion reductions in clonal fecundity.","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83592153","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
Using Integral Projection Models to Explore Management Strategies for Silver Carp (Hypophthalmichthys molitrix) 利用积分投影模型探讨鲢鱼的养殖管理策略
Spora : a journal of biomathematics Pub Date : 2023-01-01 DOI: 10.30707/spora9.1.1681910439.35821
Cameron Coles, Elizabeth Balas, J. Peirce, G. Sandland, Richard Erickson
{"title":"Using Integral Projection Models to Explore Management Strategies for Silver Carp (Hypophthalmichthys molitrix)","authors":"Cameron Coles, Elizabeth Balas, J. Peirce, G. Sandland, Richard Erickson","doi":"10.30707/spora9.1.1681910439.35821","DOIUrl":"https://doi.org/10.30707/spora9.1.1681910439.35821","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"109 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79213547","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
On Efficacy and Effectiveness of Vaccines: A Mathematical Approach Based on Conditional Probability with Applications to the COVID-19 Context 疫苗的功效和有效性:一种基于条件概率的数学方法及其在新冠肺炎疫情中的应用
Spora : a journal of biomathematics Pub Date : 2022-01-01 DOI: 10.30707/spora8.1.1652717156.639924
{"title":"On Efficacy and Effectiveness of Vaccines: A Mathematical Approach Based on Conditional Probability with Applications to the COVID-19 Context","authors":"","doi":"10.30707/spora8.1.1652717156.639924","DOIUrl":"https://doi.org/10.30707/spora8.1.1652717156.639924","url":null,"abstract":"","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86219966","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: 1
Humans vs. Zombies: Data-driven Modeling of Disease Spread 人类vs.僵尸:疾病传播的数据驱动模型
Spora : a journal of biomathematics Pub Date : 2022-01-01 DOI: 10.30707/spora8.1.1664052111.377374
Ognyan Simeonov, Kari Lemelin Fliss, J. Driscoll, C. Eaton
{"title":"Humans vs. Zombies: Data-driven Modeling of Disease Spread","authors":"Ognyan Simeonov, Kari Lemelin Fliss, J. Driscoll, C. Eaton","doi":"10.30707/spora8.1.1664052111.377374","DOIUrl":"https://doi.org/10.30707/spora8.1.1664052111.377374","url":null,"abstract":"Disease spread in close-knit communities depends heavily on the natural immunity of the individuals in the community as well as on the individuals’ interactions within the environment. This study uses data from a game of tag called Humans vs. Zombies, played on a small liberal arts campus, to examine how this “human element” can affect the spread of diseases in such communities. We fit five disease models to our data and find the best-fit parameters for each model. We conclude that an SIR model with multiple susceptibility classes and sleep cycles modifications provides the best fit, showing that human behavior is an essential element in disease modeling and that the diurnal routine of the individuals plays an important role in disease spread. Other college campuses could model similar games to observe how different cultures of people affect the results, which also doubles as a fun student engagement opportunity.","PeriodicalId":92725,"journal":{"name":"Spora : a journal of biomathematics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91321572","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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