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Koverage: Read-coverage analysis for massive(meta)genomics datasets Koverage：海量（元）基因组学数据集的读数覆盖率分析
Journal of Open Source Software Pub Date : 2024-02-27 DOI: 10.21105/joss.06235
M. Roach, Bradley J. Hart, Sarah J. Beecroft, B. Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, G. Bouras, Rob A. Edwards
{"title":"Koverage: Read-coverage analysis for massive\u0000(meta)genomics datasets","authors":"M. Roach, Bradley J. Hart, Sarah J. Beecroft, B. Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, G. Bouras, Rob A. Edwards","doi":"10.21105/joss.06235","DOIUrl":"https://doi.org/10.21105/joss.06235","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"41 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425405","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
BGmisc: An R Package for Extended Behavior GeneticsAnalysis BGmisc：用于扩展行为遗传分析的 R 软件包
Journal of Open Source Software Pub Date : 2024-02-24 DOI: 10.21105/joss.06203
S. M. Garrison, Michael D. Hunter, Xuanyu Lyu, Jonathan D. Trattner, S. A. Burt
{"title":"BGmisc: An R Package for Extended Behavior Genetics\u0000Analysis","authors":"S. M. Garrison, Michael D. Hunter, Xuanyu Lyu, Jonathan D. Trattner, S. A. Burt","doi":"10.21105/joss.06203","DOIUrl":"https://doi.org/10.21105/joss.06203","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"41 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140435029","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
stemflow: A Python Package for Adaptive Spatio-TemporalExploratory Model 茎流：用于自适应时空探索模型的 Python 软件包
Journal of Open Source Software Pub Date : 2024-02-23 DOI: 10.21105/joss.06158
Yangkang Chen, Zhongru Gu, Xiangjiang Zhan
{"title":"stemflow: A Python Package for Adaptive Spatio-Temporal\u0000Exploratory Model","authors":"Yangkang Chen, Zhongru Gu, Xiangjiang Zhan","doi":"10.21105/joss.06158","DOIUrl":"https://doi.org/10.21105/joss.06158","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"21 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140435998","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
Akantu: an HPC finite-element library for contact anddynamic fracture simulations Akantu：用于接触和动态断裂模拟的高性能计算有限元库
Journal of Open Source Software Pub Date : 2024-02-22 DOI: 10.21105/joss.05253
N. Richart, G. Anciaux, E. Gallyamov, L. Frérot, David Kammer, Mohit Pundir, Marco Vocialta, A. C. Ramos, Mauro Corrado, Philip Müller, Fabian Barras, Shenghan Zhang, Roxane Ferry, Shad Durussel, J-F Molinari
{"title":"Akantu: an HPC finite-element library for contact and\u0000dynamic fracture simulations","authors":"N. Richart, G. Anciaux, E. Gallyamov, L. Frérot, David Kammer, Mohit Pundir, Marco Vocialta, A. C. Ramos, Mauro Corrado, Philip Müller, Fabian Barras, Shenghan Zhang, Roxane Ferry, Shad Durussel, J-F Molinari","doi":"10.21105/joss.05253","DOIUrl":"https://doi.org/10.21105/joss.05253","url":null,"abstract":"the heart of modern research in mechanics of materials. For example, the buildup and release of elastic energy at geological fault is what causes earthquakes, and the intricate details of the slip zone, the propagation of slip fronts and waves radiated through the various geological media are still active areas of research","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140440642","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
helios: An R package to process heating and coolingdegrees for GCAM helios：为 GCAM 处理加热和冷却度的 R 软件包
Journal of Open Source Software Pub Date : 2024-02-22 DOI: 10.21105/joss.06033
Mengqi Zhao, Zarrar Khan, K. Dorheim, Chris Vernon
{"title":"helios: An R package to process heating and cooling\u0000degrees for GCAM","authors":"Mengqi Zhao, Zarrar Khan, K. Dorheim, Chris Vernon","doi":"10.21105/joss.06033","DOIUrl":"https://doi.org/10.21105/joss.06033","url":null,"abstract":"electricity","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"15 s1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140439859","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
Stokesian Dynamics in Python Python 中的斯托克斯动力学
Journal of Open Source Software Pub Date : 2024-02-22 DOI: 10.21105/joss.06011
A. Townsend
{"title":"Stokesian Dynamics in Python","authors":"A. Townsend","doi":"10.21105/joss.06011","DOIUrl":"https://doi.org/10.21105/joss.06011","url":null,"abstract":"Summary Stokesian Dynamics (Brady & Bossis, 1988) is a microhydrodynamic, low Reynolds number approach to modelling the movement of suspensions of particles in fluids, which considers the interaction of particles with each other against a Newtonian background solvent. It is typically chosen for its suitability for three-dimensional simulation with low calculation and time penalty. In the most basic case, Stokes’ law states that a single sphere of radius 𝑎 , travelling with a velocity 𝑈 in an unbounded Newtonian fluid of viscosity 𝜇 , in a low Reynolds number regime, experiences a drag force, 𝐹 , of 𝐹 = −6𝜋𝜇𝑎𝑈 . Stokesian Dynamics, at its heart, is an extension of this linear relationship between the force acting on a particle and the velocity at which it travels. As a method, it is adaptable and continues to be used in the field, providing interesting insight into the behaviour of particle suspensions. Validations with experiments have shown it to provide results within acceptable error. The","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"81 1‐2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140440052","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 GPU-Accelerated Open-Source Python Package forCalculating Powder Diffraction, Small-Angle-, and Total Scattering withthe Debye Scattering Equation 利用德拜散射方程计算粉末衍射、小角度和总散射的 GPU 加速开源 Python 软件包
Journal of Open Source Software Pub Date : 2024-02-20 DOI: 10.21105/joss.06024
Frederik L. Johansen, A. Anker, Ulrik Friis-Jensen, Erik B. Dam, Kirsten M Ø Jensen, Raghavendra Selvan
{"title":"A GPU-Accelerated Open-Source Python Package for\u0000Calculating Powder Diffraction, Small-Angle-, and Total Scattering with\u0000the Debye Scattering Equation","authors":"Frederik L. Johansen, A. Anker, Ulrik Friis-Jensen, Erik B. Dam, Kirsten M Ø Jensen, Raghavendra Selvan","doi":"10.21105/joss.06024","DOIUrl":"https://doi.org/10.21105/joss.06024","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"150 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140449285","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
kinisi: Bayesian analysis of mass transport frommolecular dynamics simulations kinisi：分子动力学模拟质量输运的贝叶斯分析
Journal of Open Source Software Pub Date : 2024-02-19 DOI: 10.21105/joss.05984
Andrew R. McCluskey, Alexander G. Squires, Josh Dunn, Samuel W. Coles, Benjamin J. Morgan
{"title":"kinisi: Bayesian analysis of mass transport from\u0000molecular dynamics simulations","authors":"Andrew R. McCluskey, Alexander G. Squires, Josh Dunn, Samuel W. Coles, Benjamin J. Morgan","doi":"10.21105/joss.05984","DOIUrl":"https://doi.org/10.21105/joss.05984","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"24 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140450457","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
growR: R Implementation of the Vegetation ModelModVege growR：植被模型 ModVege 的 R 实现
Journal of Open Source Software Pub Date : 2024-02-15 DOI: 10.21105/joss.06260
Kevin P. Kramer, Pierluigi Calanca
{"title":"growR: R Implementation of the Vegetation Model\u0000ModVege","authors":"Kevin P. Kramer, Pierluigi Calanca","doi":"10.21105/joss.06260","DOIUrl":"https://doi.org/10.21105/joss.06260","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"659 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139835786","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
growR: R Implementation of the Vegetation ModelModVege growR：植被模型 ModVege 的 R 实现
Journal of Open Source Software Pub Date : 2024-02-15 DOI: 10.21105/joss.06260
Kevin P. Kramer, Pierluigi Calanca
{"title":"growR: R Implementation of the Vegetation Model\u0000ModVege","authors":"Kevin P. Kramer, Pierluigi Calanca","doi":"10.21105/joss.06260","DOIUrl":"https://doi.org/10.21105/joss.06260","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"36 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139775943","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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