Research output: Contribution to journal › Article › peer-review
BioUML : an integrated environment for systems biology and collaborative analysis of biomedical data. / Kolpakov, Fedor; Akberdin, Ilya; Kashapov, Timur et al.
In: Nucleic Acids Research, Vol. 47, No. W1, 01.07.2019, p. W225-W233.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - BioUML
T2 - an integrated environment for systems biology and collaborative analysis of biomedical data
AU - Kolpakov, Fedor
AU - Akberdin, Ilya
AU - Kashapov, Timur
AU - Kiselev, Llya
AU - Kolmykov, Semyon
AU - Kondrakhin, Yury
AU - Kutumova, Elena
AU - Mandrik, Nikita
AU - Pintus, Sergey
AU - Ryabova, Anna
AU - Sharipov, Ruslan
AU - Yevshin, Ivan
AU - Kel, Alexander
N1 - © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2019/7/1
Y1 - 2019/7/1
N2 - 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.
AB - 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.
KW - FACTOR-BINDING SITES
KW - STOCHASTIC SIMULATION
KW - MODULAR MODEL
KW - SOFTWARE
KW - TOOL
KW - CIRCULATION
KW - GENENET
UR - http://www.scopus.com/inward/record.url?scp=85069238519&partnerID=8YFLogxK
U2 - 10.1093/nar/gkz440
DO - 10.1093/nar/gkz440
M3 - Article
C2 - 31131402
AN - SCOPUS:85069238519
VL - 47
SP - W225-W233
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - W1
ER -
ID: 20879170