Standard

BioUML—towards a universal research platform. / Колпаков, Федор; Акбердин, Илья Ринатович; Киселев, Илья et al.

In: Nucleic Acids Research, Vol. 50, No. W1, 05.07.2022, p. W124-W131.

Research output: Contribution to journal › Article › peer-review

Harvard

Колпаков, Ф, Акбердин, ИР, Киселев, И, Колмыков, СК, Кондрахин, Ю, Куляшов, МА, Кутумова, Е, Пинтус, СС, Рябова, А, Шарипов, РН, Евшин, И, Жатченко, С & Кель, А 2022, 'BioUML—towards a universal research platform', Nucleic Acids Research, vol. 50, no. W1, pp. W124-W131. https://doi.org/10.1093/nar/gkac286

APA

Колпаков, Ф., Акбердин, И. Р., Киселев, И., Колмыков, С. К., Кондрахин, Ю., Куляшов, М. А., Кутумова, Е., Пинтус, С. С., Рябова, А., Шарипов, Р. Н., Евшин, И., Жатченко, С., & Кель, А. (2022). BioUML—towards a universal research platform. Nucleic Acids Research, 50(W1), W124-W131. https://doi.org/10.1093/nar/gkac286

Vancouver

Колпаков Ф, Акбердин ИР, Киселев И, Колмыков СК, Кондрахин Ю, Куляшов МА et al. BioUML—towards a universal research platform. Nucleic Acids Research. 2022 Jul 5;50(W1):W124-W131. Epub 2022 May 10. doi: 10.1093/nar/gkac286

Author

Колпаков, Федор ; Акбердин, Илья Ринатович ; Киселев, Илья et al. / BioUML—towards a universal research platform. In: Nucleic Acids Research. 2022 ; Vol. 50, No. W1. pp. W124-W131.

BibTeX

@article{cd7534c19e85485aa56224c2fab8545f,
title = "BioUML—towards a universal research platform",
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.",
author = "Федор Колпаков and Акбердин, {Илья Ринатович} and Илья Киселев and Колмыков, {Семён Константинович} and Юрий Кондрахин and Куляшов, {Михаил Андреевич} and Елена Кутумова and Пинтус, {Сергей Сергеевич} and Анна Рябова and Шарипов, {Руслан Нильевич} and Иван Евшин and Сергей Жатченко and Александр Кель",
note = "Russian Science Foundation [19-72-20114 to F.K., I.K., in part, part of work related to architectural development of BioUML and development of platform for the Super charm-tau factory]; Sirius University [part of work, related to biological use cases in BioUML]. Funding for open access charge: Russian Science Foundation [19-72-20114]. Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",
year = "2022",
month = jul,
day = "5",
doi = "10.1093/nar/gkac286",
language = "English",
volume = "50",
pages = "W124--W131",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "W1",

}

RIS

TY - JOUR

T1 - BioUML—towards a universal research platform

AU - Колпаков, Федор

AU - Акбердин, Илья Ринатович

AU - Киселев, Илья

AU - Колмыков, Семён Константинович

AU - Кондрахин, Юрий

AU - Куляшов, Михаил Андреевич

AU - Кутумова, Елена

AU - Пинтус, Сергей Сергеевич

AU - Рябова, Анна

AU - Шарипов, Руслан Нильевич

AU - Евшин, Иван

AU - Жатченко, Сергей

AU - Кель, Александр

N1 - Russian Science Foundation [19-72-20114 to F.K., I.K., in part, part of work related to architectural development of BioUML and development of platform for the Super charm-tau factory]; Sirius University [part of work, related to biological use cases in BioUML]. Funding for open access charge: Russian Science Foundation [19-72-20114]. Publisher Copyright: © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2022/7/5

Y1 - 2022/7/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85130275098&partnerID=8YFLogxK

UR - https://pubmed.ncbi.nlm.nih.gov/35536253/

UR - https://www.mendeley.com/catalogue/bfc21bb8-1903-3dcd-9462-ca7c3d87a2c0/

U2 - 10.1093/nar/gkac286

DO - 10.1093/nar/gkac286

M3 - Article

C2 - 35536253

VL - 50

SP - W124-W131

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -

ID: 36188989