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. 2022 Jul 5;50(W1):W124-W131.
doi: 10.1093/nar/gkac286.

BioUML-towards a universal research platform

Fedor Kolpakov  1   2   3 , Ilya Akberdin  1   4   5 , Ilya Kiselev  1   2   3 , Semyon Kolmykov  1   4 , Yury Kondrakhin  2   4 , Mikhail Kulyashov  4 , Elena Kutumova  1   2 , Sergey Pintus  1 , Anna Ryabova  1 , Ruslan Sharipov  1   4   5 , Ivan Yevshin  1   4 , Sergey Zhatchenko  1   4 , Alexander Kel  4   6
Affiliations

BioUML-towards a universal research platform

Fedor Kolpakov et al. Nucleic Acids Res. .

Abstract

BioUML (https://www.biouml.org)-is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrated with git repositories where users can store their models and other data. We have also expanded the capabilities of BioUML for data analysis and visualization of biomedical data: (i) any programs and Jupyter kernels can be plugged into the BioUML platform using Docker technology; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks): scripts can be executed on the BioUML web pages, and BioUML functions can be called from scripts; (iv) using plug-in architecture, specialized viewers and editors can be added. For example, powerful genome browsers as well as viewers for molecular 3D structure are integrated in this way; (v) BioUML supports data analyses using workflows (own format, Galaxy, CWL, BPMN, nextFlow). Using these capabilities, we have initiated a new branch of the BioUML development-u-science-a universal scientific platform that can be configured for specific research requirements.

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Figures

Graphical Abstract
Graphical Abstract
BioUML is a complex web-based platform for systems biology and data analysis integrated with Jupyter notebook, R/Bioconductor, Galaxy and Docker technologies.
Figure 1.
Figure 1.
Architecture of the BioUML (u-science) platform. See its detailed description in the main text below.
See this image and copyright information in PMC

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References

    1. Kolpakov F., Akberdin I., Kashapov T., Kiselev L., Kolmykov S., Kondrakhin Y., Kutumova E., Mandrik N., Pintus S., Ryabova A.et al. .. BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. 2019; 47:W225–W233. - PMC - PubMed
    1. Anderson C. Docker [software engineering. IEEE Softw. 2015; 32:102–c3.
    1. Davies A., Hooley F., Causey-Freeman P., Eleftheriou I., Moulton G.. Using interactive digital notebooks for bioscience and informatics education. PLoS Comput. Biol. 2020; 16:e1008326. - PMC - PubMed
    1. Chacon S., Straub B.. Pro git. 2014; Berlin, Germany: Springer Nature.
    1. Ragan-Kelley B., Willing C.. Akici F., Lippa D., Niederhut D., Pacer M.. Binder 2.0-Reproducible, interactive, sharable environments for science at scale. Proceedings of the 17th Python in Science Conference. 2018; 113–120.

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