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harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats. harmonize-wq：将水质门户网站的数据标准化、清理和整理成更易于分析的格式。
Journal of open source software Pub Date : 2024-10-22 DOI: 10.21105/joss.07305
Justin Bousquin, Cristina A Mullin
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引用次数: 0
primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other. primerForge：一个Python程序，用于识别能够区分基因组组的引物对。
Journal of open source software Pub Date : 2024-09-16 DOI: 10.21105/joss.06850
Joseph S Wirth, Lee S Katz, Grant M Williams, Jessica C Chen
{"title":"primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.","authors":"Joseph S Wirth, Lee S Katz, Grant M Williams, Jessica C Chen","doi":"10.21105/joss.06850","DOIUrl":"10.21105/joss.06850","url":null,"abstract":"<p><p>In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An \"ingroup\" refers to a group of microbes that are the primary focus of study or interest. Conversely, an \"outgroup\" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 101","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775945","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
small_gicp: Efficient and parallel algorithms for pointcloud registration small_gicp：点云注册的高效并行算法
Journal of open source software Pub Date : 2024-08-10 DOI: 10.21105/joss.06948
Kenji Koide
{"title":"small_gicp: Efficient and parallel algorithms for point\u0000cloud registration","authors":"Kenji Koide","doi":"10.21105/joss.06948","DOIUrl":"https://doi.org/10.21105/joss.06948","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920298","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
gollum: An intuitive programmatic and visual interfacefor precomputed synthetic spectral model grids 咕噜：预计算合成光谱模型网格的直观编程和视觉界面
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06601
Sujay Shankar, M. Gully-Santiago, Caroline V. Morley, Jiayi Cao, Kyle F. Kaplan, Karina Kimani-Stewart, Diana Gonzalez-Argúeta
{"title":"gollum: An intuitive programmatic and visual interface\u0000for precomputed synthetic spectral model grids","authors":"Sujay Shankar, M. Gully-Santiago, Caroline V. Morley, Jiayi Cao, Kyle F. Kaplan, Karina Kimani-Stewart, Diana Gonzalez-Argúeta","doi":"10.21105/joss.06601","DOIUrl":"https://doi.org/10.21105/joss.06601","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"2 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921486","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
regional-mom6: A Python package for automaticgeneration of regional configurations for the Modular Ocean Model6 regional-mom6：用于自动生成模块海洋模式 6 区域配置的 Python 软件包
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06857
Ashley J. Barnes, Navid C. Constantinou, A. Gibson, A. Kiss, Chris Chapman, John Reilly, Dhruv Bhagtani, Luwei Yang
{"title":"regional-mom6: A Python package for automatic\u0000generation of regional configurations for the Modular Ocean Model\u00006","authors":"Ashley J. Barnes, Navid C. Constantinou, A. Gibson, A. Kiss, Chris Chapman, John Reilly, Dhruv Bhagtani, Luwei Yang","doi":"10.21105/joss.06857","DOIUrl":"https://doi.org/10.21105/joss.06857","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"48 49","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923956","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
ExoTiC-LD: thirty seconds to stellar limb-darkeningcoefficients ExoTiC-LD：30 秒恒星边缘致暗系数
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06816
D. Grant, H. Wakeford
{"title":"ExoTiC-LD: thirty seconds to stellar limb-darkening\u0000coefficients","authors":"D. Grant, H. Wakeford","doi":"10.21105/joss.06816","DOIUrl":"https://doi.org/10.21105/joss.06816","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"4 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921851","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
XRTpy: A Hinode-X-Ray Telescope Python Package XRTpy：日冕-X 射线望远镜 Python 软件包
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06396
Joy Velasquez, Nicholas Murphy, Katharine K. Reeves, Jonathan Slavin, Mark Weber, Will T. Barnes
{"title":"XRTpy: A Hinode-X-Ray Telescope Python Package","authors":"Joy Velasquez, Nicholas Murphy, Katharine K. Reeves, Jonathan Slavin, Mark Weber, Will T. Barnes","doi":"10.21105/joss.06396","DOIUrl":"https://doi.org/10.21105/joss.06396","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"49 42","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923930","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
SIRITVIS: Social Interaction Research Insights TopicVisualisation SIRITVIS：社会互动研究洞察主题可视化
Journal of open source software Pub Date : 2024-08-08 DOI: 10.21105/joss.06243
Sagar Narwade, Gillian Kant, Benjamin Säfken, Benjamin Leiding
{"title":"SIRITVIS: Social Interaction Research Insights Topic\u0000Visualisation","authors":"Sagar Narwade, Gillian Kant, Benjamin Säfken, Benjamin Leiding","doi":"10.21105/joss.06243","DOIUrl":"https://doi.org/10.21105/joss.06243","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"56 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929215","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
SOUPy: Stochastic PDE-constrained optimization underhigh-dimensional uncertainty in Python SOUPy：Python 中高维不确定性下的随机 PDE 受限优化
Journal of open source software Pub Date : 2024-07-28 DOI: 10.21105/joss.06101
Dingcheng Luo, Peng Chen, Thomas O'Leary-Roseberry, Umberto Villa, Omar Ghattas
{"title":"SOUPy: Stochastic PDE-constrained optimization under\u0000high-dimensional uncertainty in Python","authors":"Dingcheng Luo, Peng Chen, Thomas O'Leary-Roseberry, Umberto Villa, Omar Ghattas","doi":"10.21105/joss.06101","DOIUrl":"https://doi.org/10.21105/joss.06101","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"10 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141796452","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
hf_hydrodata: A Python package for accessing hydrologicsimulations and observations across the United States hf_hydrodata：用于访问全美水文模拟和观测数据的 Python 软件包
Journal of open source software Pub Date : 2024-07-26 DOI: 10.21105/joss.06623
Amy Defnet, William Hasling, Laura Condon, Amy Johnson, Georgios Artavanis, Amanda Triplett, William Lytle, Reed Maxwell
{"title":"hf_hydrodata: A Python package for accessing hydrologic\u0000simulations and observations across the United States","authors":"Amy Defnet, William Hasling, Laura Condon, Amy Johnson, Georgios Artavanis, Amanda Triplett, William Lytle, Reed Maxwell","doi":"10.21105/joss.06623","DOIUrl":"https://doi.org/10.21105/joss.06623","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141799248","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
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