BioUML—towards a universal research platform

Федор Колпаков, Илья Ринатович Акбердин, Илья Киселев, Семён Константинович Колмыков, Юрий Кондрахин, Михаил Андреевич Куляшов, Елена Кутумова, Сергей Сергеевич Пинтус, Анна Рябова, Руслан Нильевич Шарипов, Иван Евшин, Сергей Жатченко, Александр Кель

Результат исследования: Научные публикации в периодических изданияхстатьярецензирование

Аннотация

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.
Язык оригиналаанглийский
Страницы (с-по)W124-W131
Число страниц8
ЖурналNucleic Acids Research
Том50
Номер выпускаW1
DOI
СостояниеОпубликовано - 5 июл 2022

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