{"title":"SonoUno development: a User-Centered Sonification\u0000software for data analysis","authors":"J. Casado, G. de la Vega, Beatriz García","doi":"10.21105/joss.05819","DOIUrl":"https://doi.org/10.21105/joss.05819","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139601299","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}
Robrecht Cannoodt, Hendrik Cannoodt, Dries Schaumont, Kai Waldrant, Eric Van de Kerckhove, Andy Boschmans, D. D. Maeyer, Toni Verbeiren
Most bioinformatics workflows consist of software components that are tightly coupled to the logic of the workflow itself. This limits reusability of the individual components in the workflow or introduces maintenance overhead when they need to be reimplemented in multiple workflows. We introduce Viash, a tool for speeding up development of robust workflows through “code-first” prototyping, separation of concerns and code generation of modular workflow components. By decoupling the component functionality from the workflow logic, component functionality becomes fully workflow-agnostic, and conversely the resulting workflows are agnostic towards specific component requirements. This separation of concerns improves reusability of components and facilitates multidisciplinary and pan-organisational collaborations. It has been applied in a variety of projects, from proof-of-concept workflows to supporting an international data science competition. Viash is available as an open-source project at github.com/viash-io/viash and documentation is available at viash.io
{"title":"Viash: A meta-framework for building reusable workflow\u0000modules","authors":"Robrecht Cannoodt, Hendrik Cannoodt, Dries Schaumont, Kai Waldrant, Eric Van de Kerckhove, Andy Boschmans, D. D. Maeyer, Toni Verbeiren","doi":"10.21105/joss.06089","DOIUrl":"https://doi.org/10.21105/joss.06089","url":null,"abstract":"Most bioinformatics workflows consist of software components that are tightly coupled to the logic of the workflow itself. This limits reusability of the individual components in the workflow or introduces maintenance overhead when they need to be reimplemented in multiple workflows. We introduce Viash, a tool for speeding up development of robust workflows through “code-first” prototyping, separation of concerns and code generation of modular workflow components. By decoupling the component functionality from the workflow logic, component functionality becomes fully workflow-agnostic, and conversely the resulting workflows are agnostic towards specific component requirements. This separation of concerns improves reusability of components and facilitates multidisciplinary and pan-organisational collaborations. It has been applied in a variety of projects, from proof-of-concept workflows to supporting an international data science competition. Viash is available as an open-source project at github.com/viash-io/viash and documentation is available at viash.io","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139602210","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}
Exposure to environmental noise can have significant health effects, including environmental sleep disorders, hypertension, ischemic heart disease, and stroke. Accurately predicting sound levels and estimating health risks is critical to studying the exposure-response relationships and formulating effective policies at the local community level. However, such predictions typically require specialized knowledge, expensive commercial software, and extensive computational resources. To address this issue, the author has developed a solution that integrates publicly available vector tile maps, open source environmental noise modeling modules called “Noise-Modelling”, and user interfaces implemented in QGIS through a dedicated QGIS plugin. This plugin allows for direct execution of the calculation modules implemented in NoiseModelling, ensuring compatibility with future updates to NoiseModelling. Users can easily access and manipulate geographic features, define receiver points, predict sound levels, and estimate health risks for any desired area using the plugin. For a relatively small computational domain, such as 1 km2, the volume of calculations is manageable and can be performed on a local computer. This plugin is invaluable for conducting epidemiological research on the health effects of environmental noise and for noise policy planning. It facilitates the maintenance of a quiet environment, helps to mitigate noise problems, and aids in estimating the noise generated by new sources.
{"title":"H-RISK with NoiseModelling: a QGIS plugin to predict\u0000environmental noise and estimate health risks","authors":"Junta Tagusari","doi":"10.21105/joss.06023","DOIUrl":"https://doi.org/10.21105/joss.06023","url":null,"abstract":"Exposure to environmental noise can have significant health effects, including environmental sleep disorders, hypertension, ischemic heart disease, and stroke. Accurately predicting sound levels and estimating health risks is critical to studying the exposure-response relationships and formulating effective policies at the local community level. However, such predictions typically require specialized knowledge, expensive commercial software, and extensive computational resources. To address this issue, the author has developed a solution that integrates publicly available vector tile maps, open source environmental noise modeling modules called “Noise-Modelling”, and user interfaces implemented in QGIS through a dedicated QGIS plugin. This plugin allows for direct execution of the calculation modules implemented in NoiseModelling, ensuring compatibility with future updates to NoiseModelling. Users can easily access and manipulate geographic features, define receiver points, predict sound levels, and estimate health risks for any desired area using the plugin. For a relatively small computational domain, such as 1 km2, the volume of calculations is manageable and can be performed on a local computer. This plugin is invaluable for conducting epidemiological research on the health effects of environmental noise and for noise policy planning. It facilitates the maintenance of a quiet environment, helps to mitigate noise problems, and aids in estimating the noise generated by new sources.","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139605427","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}
M. Weiner, Christoph Renzing, Max Stirl, M. Schmidtchen, Ulrich Prahl
{"title":"PyRolL - An Extensible OpenSource Framework for Rolling\u0000Simulation","authors":"M. Weiner, Christoph Renzing, Max Stirl, M. Schmidtchen, Ulrich Prahl","doi":"10.21105/joss.06200","DOIUrl":"https://doi.org/10.21105/joss.06200","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139604714","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}
K. Schmidt, A. Scourtas, Logan Ward, Steve Wangen, Marcus Schwarting, Isaac Darling, Ethan Truelove, Aadit Ambadkar, Ribhav Bose, Zoa Katok, Jingrui Wei, Xiangguo Li, R. Jacobs, Lane Schultz, Doyeon Kim, Michael Ferris, P. Voyles, Dane Morgan, Ian Foster, B. Blaiszik
. Artificial Intelligence
.人工智能
{"title":"Foundry-ML - Software and Services to Simplify Access\u0000to Machine Learning Datasets in Materials Science","authors":"K. Schmidt, A. Scourtas, Logan Ward, Steve Wangen, Marcus Schwarting, Isaac Darling, Ethan Truelove, Aadit Ambadkar, Ribhav Bose, Zoa Katok, Jingrui Wei, Xiangguo Li, R. Jacobs, Lane Schultz, Doyeon Kim, Michael Ferris, P. Voyles, Dane Morgan, Ian Foster, B. Blaiszik","doi":"10.21105/joss.05467","DOIUrl":"https://doi.org/10.21105/joss.05467","url":null,"abstract":". Artificial Intelligence","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139604056","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":"cstag and cstag-cli: tools for manipulating and\u0000visualizing cs tags","authors":"Akihiro Kuno","doi":"10.21105/joss.06066","DOIUrl":"https://doi.org/10.21105/joss.06066","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139607813","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":"The Kestrel software for simulations of morphodynamic\u0000Earth-surface flows","authors":"Jake Langham, M. Woodhouse","doi":"10.21105/joss.06079","DOIUrl":"https://doi.org/10.21105/joss.06079","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139608422","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}
Thomas R. Else, J. Gröhl, Lina Hacker, S. Bohndiek
{"title":"PATATO: a Python photoacoustic tomography analysis\u0000toolkit","authors":"Thomas R. Else, J. Gröhl, Lina Hacker, S. Bohndiek","doi":"10.21105/joss.05686","DOIUrl":"https://doi.org/10.21105/joss.05686","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139613051","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":"pymatgen-analysis-defects: A Python package for\u0000analyzing point defects in crystalline materials","authors":"Jimmy-Xuan Shen, J. Varley","doi":"10.21105/joss.05941","DOIUrl":"https://doi.org/10.21105/joss.05941","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139611810","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":"quantile-forest: A Python Package for Quantile\u0000Regression Forests","authors":"Reid A. Johnson","doi":"10.21105/joss.05976","DOIUrl":"https://doi.org/10.21105/joss.05976","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139613232","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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