Sean Matthew, Fin Carter, Joshua Cooper, Matthew Dippel, Ethan Green, Samuel Hodges, Mason Kidwell, Dalton Nickerson, Bryan Rumsey, Jesse Reeve, Linda R Petzold, Kevin R Sanft, Brian Drawert
Stochastic modeling has become an essential tool for studying biochemical reaction networks. There is a growing need for user-friendly and feature-complete software for model design and simulation. To address this need, we present GillesPy2, an open-source framework for building and simulating mathematical and biochemical models. GillesPy2, a major upgrade from the original GillesPy package, is now a stand-alone Python 3 package. GillesPy2 offers an intuitive interface for robust and reproducible model creation, facilitating rapid and iterative development. In addition to expediting the model creation process, GillesPy2 offers efficient algorithms to simulate stochastic, deterministic, and hybrid stochastic-deterministic models.
{"title":"GillesPy2: A Biochemical Modeling Framework for Simulation Driven Biological Discovery.","authors":"Sean Matthew, Fin Carter, Joshua Cooper, Matthew Dippel, Ethan Green, Samuel Hodges, Mason Kidwell, Dalton Nickerson, Bryan Rumsey, Jesse Reeve, Linda R Petzold, Kevin R Sanft, Brian Drawert","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Stochastic modeling has become an essential tool for studying biochemical reaction networks. There is a growing need for user-friendly and feature-complete software for model design and simulation. To address this need, we present GillesPy2, an open-source framework for building and simulating mathematical and biochemical models. GillesPy2, a major upgrade from the original GillesPy package, is now a stand-alone Python 3 package. GillesPy2 offers an intuitive interface for robust and reproducible model creation, facilitating rapid and iterative development. In addition to expediting the model creation process, GillesPy2 offers efficient algorithms to simulate stochastic, deterministic, and hybrid stochastic-deterministic models.</p>","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"10 1","pages":"87-103"},"PeriodicalIF":0.0,"publicationDate":"2023-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10470263/pdf/nihms-1921950.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10148803","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 : 2023-01-01DOI: 10.30707/lib10.1.1682014077.7837
{"title":"Welcome to Volume 10","authors":"","doi":"10.30707/lib10.1.1682014077.7837","DOIUrl":"https://doi.org/10.30707/lib10.1.1682014077.7837","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577029","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}
Pub Date : 2023-01-01DOI: 10.30707/lib10.1.1682014077.806265
{"title":"Mathematical Analysis and Parameter Estimation of a Two-Patch Zika Model","authors":"","doi":"10.30707/lib10.1.1682014077.806265","DOIUrl":"https://doi.org/10.30707/lib10.1.1682014077.806265","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577107","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}
Pub Date : 2023-01-01DOI: 10.30707/lib10.1.1682014077.8265
{"title":"Modeling the Spread of Curly Top Disease in Tomatoes","authors":"","doi":"10.30707/lib10.1.1682014077.8265","DOIUrl":"https://doi.org/10.30707/lib10.1.1682014077.8265","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577773","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}
Pub Date : 2023-01-01DOI: 10.30707/lib10.1.1684158870.855659
Brandon Grandison, Hannah Yin, Ana Kilgore, Matthew J. Young, Jing Jiao, Nina H. Feerman
Evolutionary game theory (EGT) analyzes the stability of competing strategies for withstanding selective pressures within a population over generations. Under rapid shifts in selective pressures (e
{"title":"Epidemiology, Game Theory, and Evolutionary Rescue: Understanding How Outbreaks Impact Population Viability","authors":"Brandon Grandison, Hannah Yin, Ana Kilgore, Matthew J. Young, Jing Jiao, Nina H. Feerman","doi":"10.30707/lib10.1.1684158870.855659","DOIUrl":"https://doi.org/10.30707/lib10.1.1684158870.855659","url":null,"abstract":"Evolutionary game theory (EGT) analyzes the stability of competing strategies for withstanding selective pressures within a population over generations. Under rapid shifts in selective pressures (e","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577838","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}
Pub Date : 2023-01-01DOI: 10.30707/lib6.2.1681911844.007402
Narender Kumar, S. Parveen, Ravins Dohare
In this study, we used a simple epidemic model and 2015–16 outbreak data of Chikungunya, Dengue and Zika viruses, arthropod mediated infections that are transmitted by the common mosquito vector Aedes aegypti, from Mexico to quantify the transmission rates (humans-to-mosquitoes and mosquitoes-to-humans) of the three diseases. The transmission rates are estimated for the observed data and consequently the basic reproduction number (R0) is calculated 6.740, 2.904 and 12.6283 for Chikungunya, Dengue and Zika infection, respectively. Using the estimated parameters for the three diseases, we evaluated self-imposed controls measures by the population as a result of fear-driven behavior changes often seen during an outbreak. Furthermore, the sensitivity analysis reveals that the parameter 'mosquitoes death rate' is the most sensitive one for R0. Simulations of controlled basic reproduction number are also performed for all considered control measures. This study is likely to enrich the understanding about transmission of such viral infections and control strategies.
{"title":"Comparative Transmission Dynamics and Optimal Controls for Chikungunya, Dengue and Zika Virus Infections","authors":"Narender Kumar, S. Parveen, Ravins Dohare","doi":"10.30707/lib6.2.1681911844.007402","DOIUrl":"https://doi.org/10.30707/lib6.2.1681911844.007402","url":null,"abstract":"In this study, we used a simple epidemic model and 2015–16 outbreak data of Chikungunya, Dengue and Zika viruses, arthropod mediated infections that are transmitted by the common mosquito vector Aedes aegypti, from Mexico to quantify the transmission rates (humans-to-mosquitoes and mosquitoes-to-humans) of the three diseases. The transmission rates are estimated for the observed data and consequently the basic reproduction number (R0) is calculated 6.740, 2.904 and 12.6283 for Chikungunya, Dengue and Zika infection, respectively. Using the estimated parameters for the three diseases, we evaluated self-imposed controls measures by the population as a result of fear-driven behavior changes often seen during an outbreak. Furthermore, the sensitivity analysis reveals that the parameter 'mosquitoes death rate' is the most sensitive one for R0. Simulations of controlled basic reproduction number are also performed for all considered control measures. This study is likely to enrich the understanding about transmission of such viral infections and control strategies.","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577847","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}
Pub Date : 2023-01-01DOI: 10.30707/lib8.1.1682013528.144161
{"title":"Effect of SOF/VEL Antiviral Therapy for HCV Treatment","authors":"","doi":"10.30707/lib8.1.1682013528.144161","DOIUrl":"https://doi.org/10.30707/lib8.1.1682013528.144161","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577390","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}
Pub Date : 2023-01-01DOI: 10.30707/lib6.2.1681911844.017516
Ram Singh, Naveen Sharma, Aditi Ghosh
Ebola virus is a life-threatening virus and has two major characteristics; one potential to have high mortality rate and the other infection transmission through newly infected dead bodies. There are some relevant features of Ebola that were observed during its recent outbreak: including varying rate of access to isolation facilities by patients and transmission of infection via improper handling of the dead bodies of infected diseased. Quick and safe burial may play an important role in the control and prevention of this virus. In this study, we consider mathematical modeling framework with four different cases for dynamics of Ebola virus with safe and unsafe burial practices, vaccination and treatment interventions with varying efficiency. The goal of this study is to show how timely treatment to Ebola leads to an effective control of the virus and, most importantly, how safe burial of dead bodies helps control the spread. ARTICLE HISTORY Received November 27, 2018 Accepted December 18, 2019
{"title":"Modeling Assumptions, Mathematical Analysis and Mitigation Through Intervention","authors":"Ram Singh, Naveen Sharma, Aditi Ghosh","doi":"10.30707/lib6.2.1681911844.017516","DOIUrl":"https://doi.org/10.30707/lib6.2.1681911844.017516","url":null,"abstract":"Ebola virus is a life-threatening virus and has two major characteristics; one potential to have high mortality rate and the other infection transmission through newly infected dead bodies. There are some relevant features of Ebola that were observed during its recent outbreak: including varying rate of access to isolation facilities by patients and transmission of infection via improper handling of the dead bodies of infected diseased. Quick and safe burial may play an important role in the control and prevention of this virus. In this study, we consider mathematical modeling framework with four different cases for dynamics of Ebola virus with safe and unsafe burial practices, vaccination and treatment interventions with varying efficiency. The goal of this study is to show how timely treatment to Ebola leads to an effective control of the virus and, most importantly, how safe burial of dead bodies helps control the spread. ARTICLE HISTORY Received November 27, 2018 Accepted December 18, 2019","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577381","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}
Pub Date : 2023-01-01DOI: 10.30707/lib10.1.1682535100.316029
{"title":"Substrate Transport in Cylindrical Multi-Capillary Beds with Axial Diffusion","authors":"","doi":"10.30707/lib10.1.1682535100.316029","DOIUrl":"https://doi.org/10.30707/lib10.1.1682535100.316029","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577786","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}
Pub Date : 2023-01-01DOI: 10.30707/lib9.1.1681913305.295521
{"title":"A Hybrid Differential Equations Model for the Dynamics of Single and Double Strand\u0000 Breaks of Cancer Cells Treated by Radiotherapy","authors":"","doi":"10.30707/lib9.1.1681913305.295521","DOIUrl":"https://doi.org/10.30707/lib9.1.1681913305.295521","url":null,"abstract":"","PeriodicalId":37222,"journal":{"name":"Letters in Biomathematics","volume":"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":"69577587","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}
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