SGABU computational platform for multiscale modeling: Bridging the gap between education and research

Tijana Geroski, Orestis Gkaintes, Aleksandra Vulović, Niketa Ukaj, Jorge Barrasa-Fano, Fernando Perez-Boerema, Bogdan Milićević, Aleksandar Atanasijević, Jelena Živković, Andreja Živić, Maria Roumpi, Themis Exarchos, Christian Hellmich, Stefan Scheiner, Hans Van Oosterwyck, Djordje Jakovljević, Miloš Ivanović, Nenad Filipović

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Abstract

BACKGROUND AND OBJECTIVE: In accordance with the latest aspirations in the field of bioengineering, there is a need to create a web accessible, but powerful cloud computational platform that combines datasets and multiscale models related to bone modeling, cancer, cardiovascular diseases and tissue engineering. The SGABU platform may become a powerful information system for research and education that can integrate data, extract information, and facilitate knowledge exchange with the goal of creating and developing appropriate computing pipelines to provide accurate and comprehensive biological information from the molecular to organ level. METHODS: The datasets integrated into the platform are obtained from experimental and/or clinical studies and are mainly in tabular or image file format, including metadata. The implementation of multiscale models, is an ambitious effort of the platform to capture phenomena at different length scales, described using partial and ordinary differential equations, which are solved numerically on complex geometries with the use of the finite element method. The majority of the SGABU platform's simulation pipelines are provided as Common Workflow Language (CWL) workflows. Each of them requires creating a CWL implementation on the backend and a user-friendly interface using standard web technologies. Platform is available at https://sgabu-test.unic.kg.ac.rs/login. RESULTS: The main dashboard of the SGABU platform is divided into sections for each field of research, each one of which includes a subsection of datasets and multiscale models. The datasets can be presented in a simple form as tabular data, or using technologies such as Plotly.js for 2D plot interactivity, Kitware Paraview Glance for 3D view. Regarding the models, the usage of Docker containerization for packing the individual tools and CWL orchestration for describing inputs with validation forms and outputs with tabular views for output visualization, interactive diagrams, 3D views and animations. CONCLUSIONS: In practice, the structure of SGABU platform means that any of the integrated workflows can work equally well on any other bioengineering platform. The key advantage of the SGABU platform over similar efforts is its versatility offered with the use of modern, modular, and extensible technology for various levels of architecture.

Original languageEnglish
Article number107935
Number of pages12
JournalComputer Methods and Programs in Biomedicine
Volume243
Early online date22 Nov 2023
DOIs
Publication statusPublished - 1 Jan 2024

Bibliographical note

Publisher Copyright:
Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.
This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/bync/4.0/)

Funder

This research is also supported by the project that has received funding from the European Union's Horizon 2020 research and innovation programmes under grant agreement No 952603 (SGABU project). This article reflects only the author's view. The Commission is not responsible for any use that may be made of the information it contains. T.G., A.V., B.M. and N.F. also acknowledge the funding by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia, contract number [451-03-47/2023-01/200107 (Faculty of Engineering, University of Kragujevac)].

Keywords

  • Computational platform
  • Multiscale modeling
  • Open science
  • User-friendly interface

ASJC Scopus subject areas

  • Software
  • Computer Science Applications
  • Health Informatics

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