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

Fedor Kolpakov, Ilya Akberdin, Timur Kashapov, Llya Kiselev, Semyon Kolmykov, Yury Kondrakhin, Elena Kutumova, Nikita Mandrik, Sergey Pintus, Anna Ryabova, Ruslan Sharipov, Ivan Yevshin, Alexander Kel

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)W225-W233
Number of pages9
JournalNucleic Acids Research
Volume47
Issue numberW1
DOIs
Publication statusPublished - 1 Jul 2019

Keywords

  • FACTOR-BINDING SITES
  • STOCHASTIC SIMULATION
  • MODULAR MODEL
  • SOFTWARE
  • TOOL
  • CIRCULATION
  • GENENET

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