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BioUML—towards a universal research platform
BioUML (https://www.biouml.org)—is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolis...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252820/ https://www.ncbi.nlm.nih.gov/pubmed/35536253 http://dx.doi.org/10.1093/nar/gkac286 |
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author | Kolpakov, Fedor Akberdin, Ilya Kiselev, Ilya Kolmykov, Semyon Kondrakhin, Yury Kulyashov, Mikhail Kutumova, Elena Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Zhatchenko, Sergey Kel, Alexander |
author_facet | Kolpakov, Fedor Akberdin, Ilya Kiselev, Ilya Kolmykov, Semyon Kondrakhin, Yury Kulyashov, Mikhail Kutumova, Elena Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Zhatchenko, Sergey Kel, Alexander |
author_sort | Kolpakov, Fedor |
collection | PubMed |
description | BioUML (https://www.biouml.org)—is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrated with git repositories where users can store their models and other data. We have also expanded the capabilities of BioUML for data analysis and visualization of biomedical data: (i) any programs and Jupyter kernels can be plugged into the BioUML platform using Docker technology; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks): scripts can be executed on the BioUML web pages, and BioUML functions can be called from scripts; (iv) using plug-in architecture, specialized viewers and editors can be added. For example, powerful genome browsers as well as viewers for molecular 3D structure are integrated in this way; (v) BioUML supports data analyses using workflows (own format, Galaxy, CWL, BPMN, nextFlow). Using these capabilities, we have initiated a new branch of the BioUML development—u-science—a universal scientific platform that can be configured for specific research requirements. |
format | Online Article Text |
id | pubmed-9252820 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92528202022-07-05 BioUML—towards a universal research platform Kolpakov, Fedor Akberdin, Ilya Kiselev, Ilya Kolmykov, Semyon Kondrakhin, Yury Kulyashov, Mikhail Kutumova, Elena Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Zhatchenko, Sergey Kel, Alexander Nucleic Acids Res Web Server Issue BioUML (https://www.biouml.org)—is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrated with git repositories where users can store their models and other data. We have also expanded the capabilities of BioUML for data analysis and visualization of biomedical data: (i) any programs and Jupyter kernels can be plugged into the BioUML platform using Docker technology; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks): scripts can be executed on the BioUML web pages, and BioUML functions can be called from scripts; (iv) using plug-in architecture, specialized viewers and editors can be added. For example, powerful genome browsers as well as viewers for molecular 3D structure are integrated in this way; (v) BioUML supports data analyses using workflows (own format, Galaxy, CWL, BPMN, nextFlow). Using these capabilities, we have initiated a new branch of the BioUML development—u-science—a universal scientific platform that can be configured for specific research requirements. Oxford University Press 2022-05-10 /pmc/articles/PMC9252820/ /pubmed/35536253 http://dx.doi.org/10.1093/nar/gkac286 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Kolpakov, Fedor Akberdin, Ilya Kiselev, Ilya Kolmykov, Semyon Kondrakhin, Yury Kulyashov, Mikhail Kutumova, Elena Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Zhatchenko, Sergey Kel, Alexander BioUML—towards a universal research platform |
title | BioUML—towards a universal research platform |
title_full | BioUML—towards a universal research platform |
title_fullStr | BioUML—towards a universal research platform |
title_full_unstemmed | BioUML—towards a universal research platform |
title_short | BioUML—towards a universal research platform |
title_sort | biouml—towards a universal research platform |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252820/ https://www.ncbi.nlm.nih.gov/pubmed/35536253 http://dx.doi.org/10.1093/nar/gkac286 |
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