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. 2019 Jul 2;47(W1):W225-W233.
doi: 10.1093/nar/gkz440.

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

Fedor Kolpakov  1   2 , Ilya Akberdin  1   3 , Timur Kashapov  1 , Llya Kiselev  1   2 , Semyon Kolmykov  1   2   4 , Yury Kondrakhin  1   2 , Elena Kutumova  1   2 , Nikita Mandrik  1   2 , Sergey Pintus  1   2 , Anna Ryabova  1   2 , Ruslan Sharipov  1   3 , Ivan Yevshin  1   2 , Alexander Kel  1   5   6
Affiliations

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

Fedor Kolpakov et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1.
Figure 1.
The BioUML web interface consists of: (A) repository pane, (B) document pane, (C) info pane, (D) viewer/editor pane, (E) perspective selector.
See this image and copyright information in PMC

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