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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...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
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
Descripción
Sumario: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.