BART-Survival is a Python package that allows time-to-event (survival) analyses in discrete-time using the non-parametric machine learning algorithm, Bayesian Additive Regression Trees (BART). BART-Survival combines the performance of the BART algorithm with the complementary data and model formatting required to complete the survival analyses. The library contains a convenient application programming interface (API) that allows a simple approach when using the library for survival analyses, while maintaining capabilities for added complexity when desired. The package is intended for analysts exploring use of flexible non-parametric alternatives to traditional (semi-)parametric survival analyses.
{"title":"BART-Survival: A Bayesian machine learning approach to survival analyses in Python.","authors":"Jacob Tiegs, Julia Raykin, Ilia Rochlin","doi":"10.21105/joss.07213","DOIUrl":"10.21105/joss.07213","url":null,"abstract":"<p><p>BART-Survival is a Python package that allows time-to-event (survival) analyses in discrete-time using the non-parametric machine learning algorithm, Bayesian Additive Regression Trees (BART). BART-Survival combines the performance of the BART algorithm with the complementary data and model formatting required to complete the survival analyses. The library contains a convenient application programming interface (API) that allows a simple approach when using the library for survival analyses, while maintaining capabilities for added complexity when desired. The package is intended for analysts exploring use of flexible non-parametric alternatives to traditional (semi-)parametric survival analyses.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"10 105","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495117","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}
{"title":"harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats.","authors":"Justin Bousquin, Cristina A Mullin","doi":"10.21105/joss.07305","DOIUrl":"https://doi.org/10.21105/joss.07305","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 102","pages":"7305"},"PeriodicalIF":0.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933878","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}
Joseph S Wirth, Lee S Katz, Grant M Williams, Jessica C Chen
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.
{"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}
{"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}
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}
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}
{"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}
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}
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}
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