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

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.</p

A flexible and easy-to-use open-source tool for designing functionally graded 3D porous structures

Advances in additive manufacturing technologies are leading to an increased interest in the design of intricate 3D geometries for applications ranging from aerospace to biomedical engineering. In this paper, we present ASLI (A Simple Lattice Infiller), a cross-platform tool for the generation of cellular solid structures that allows users to provide implicitly defined lattice infills to 3D objects by specifying the desired local unit cell type, size and feature. It is written in C++ and relies on the open-source libraries Mmg and CGAL to handle the implicit domain discretisation. Although developed to design lattice infills for skeletal tissue engineering applications, ASLI can be used for any application that requires the user to provide lattice infills to 3D objects. Its capabilities are shown through a series of examples that demonstrate complex designs can easily be accomplished. The code is published under an open-source license and is available for download at github.com/tpms-lattice/ASLI

A multi-scale modelling framework combining musculoskeletal rigid-body simulations with adaptive finite element analyses, to evaluate the impact of femoral geometry on hip joint contact forces and femoral bone growth

Multi-scale simulations, combining muscle and joint contact force (JCF) from musculoskeletal simulations with adaptive mechanobiological finite element analysis, allow to estimate musculoskeletal loading and predict femoral growth in children. Generic linearly scaled musculoskeletal models are commonly used. This approach, however, neglects subject- and age-specific musculoskeletal geometry, e.g. femoral neck-shaft angle (NSA) and anteversion angle (AVA). This study aimed to evaluate the impact of proximal femoral geometry, i.e. altered NSA and AVA, on hip JCF and femoral growth simulations. Musculoskeletal models with NSA ranging from 120° to 150° and AVA ranging from 20° to 50° were created and used to calculate muscle and hip JCF based on the gait analysis data of a typically developing child. A finite element model of a paediatric femur was created from magnetic resonance images. The finite element model was morphed to the geometries of the different musculoskeletal models and used for mechanobiological finite element analysis to predict femoral growth trends. Our findings showed that hip JCF increase with increasing NSA and AVA. Furthermore, the orientation of the hip JCF followed the orientation of the femoral neck axis. Consequently, the osteogenic index, which is a function of cartilage stresses and defines the growth rate, barely changed with altered NSA and AVA. Nevertheless, growth predictions were sensitive to the femoral geometry due to changes in the predicted growth directions. Altered NSA had a bigger impact on the growth results than altered AVA. Growth simulations based on mechanobiological principles were in agreement with reported changes in paediatric populations.status: publishe