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BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data
BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cel...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602424/ https://www.ncbi.nlm.nih.gov/pubmed/31131402 http://dx.doi.org/10.1093/nar/gkz440 |
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author | Kolpakov, Fedor Akberdin, Ilya Kashapov, Timur Kiselev, llya Kolmykov, Semyon Kondrakhin, Yury Kutumova, Elena Mandrik, Nikita Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Kel, Alexander |
author_facet | Kolpakov, Fedor Akberdin, Ilya Kashapov, Timur Kiselev, llya Kolmykov, Semyon Kondrakhin, Yury Kutumova, Elena Mandrik, Nikita Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Kel, Alexander |
author_sort | Kolpakov, Fedor |
collection | PubMed |
description | BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient. BioUML spans a comprehensive range of capabilities, including access to biological databases, powerful tools for systems biology (visual modelling, simulation, parameters fitting and analyses), a genome browser, scripting (R, JavaScript) and a workflow engine. Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data. The plug-in-based architecture allows the user to add new functionalities using plug-ins. To facilitate a user focus on a particular task or database, we have developed several predefined perspectives that display only those web interface elements that are needed for a specific task. To support collaborative work on scientific projects, there is a central authentication and authorization system (https://bio-store.org). The diagram editor enables several remote users to simultaneously edit diagrams. |
format | Online Article Text |
id | pubmed-6602424 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66024242019-07-05 BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data Kolpakov, Fedor Akberdin, Ilya Kashapov, Timur Kiselev, llya Kolmykov, Semyon Kondrakhin, Yury Kutumova, Elena Mandrik, Nikita Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Kel, Alexander Nucleic Acids Res Web Server Issue BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient. BioUML spans a comprehensive range of capabilities, including access to biological databases, powerful tools for systems biology (visual modelling, simulation, parameters fitting and analyses), a genome browser, scripting (R, JavaScript) and a workflow engine. Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data. The plug-in-based architecture allows the user to add new functionalities using plug-ins. To facilitate a user focus on a particular task or database, we have developed several predefined perspectives that display only those web interface elements that are needed for a specific task. To support collaborative work on scientific projects, there is a central authentication and authorization system (https://bio-store.org). The diagram editor enables several remote users to simultaneously edit diagrams. Oxford University Press 2019-07-02 2019-05-27 /pmc/articles/PMC6602424/ /pubmed/31131402 http://dx.doi.org/10.1093/nar/gkz440 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://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 Kashapov, Timur Kiselev, llya Kolmykov, Semyon Kondrakhin, Yury Kutumova, Elena Mandrik, Nikita Pintus, Sergey Ryabova, Anna Sharipov, Ruslan Yevshin, Ivan Kel, Alexander BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title | BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title_full | BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title_fullStr | BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title_full_unstemmed | BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title_short | BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data |
title_sort | biouml: an integrated environment for systems biology and collaborative analysis of biomedical data |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602424/ https://www.ncbi.nlm.nih.gov/pubmed/31131402 http://dx.doi.org/10.1093/nar/gkz440 |
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