Physics-based simulations provide a powerful framework for understanding biological form and function. They harmonize heterogeneous experimental data with real-world physical constraints, helping researchers understand biological systems as they engineer novel drugs, new diagnostics, medical devices, and surgical interventions. The rise in new sensors and simulation tools is generating an increasing amount of data, but this data is often inaccessible, preventing reuse and limiting scientific progress. In 2005, we launched SimTK, a website to develop and share biosimulation tools, models, and data, to address these issues. SimTK now supports 62,000+ researchers globally and 950+ projects. Members use it to meet their grants? data sharing responsibilities; experiment with new ways of collaborating; and build communities around their datasets and tools. However, challenges remain: many researchers still do not share their digital assets due to the time needed to prepare, document, and maintain those assets, and since SimTK hosts a growing number of diverse digital assets, the site now also faces the challenge of making these assets discoverable and reusable. Thus, we propose a plan to extend SimTK and implement new solutions to promote scientific data sharing and reuse. First, we will maintain the reliable, user-friendly foundation upon which SimTK is built, continuing to provide the excellent support our members expect and supporting the site?s existing features for sharing and building communities. Second, we will implement methods to establish a culture of model and data sharing in the biomechanics community. We will encourage researchers to adopt new habits, making sharing part of their workflow, by enabling the software and systems they use to automatically upload models and data to SimTK via an application programming interface (API) and by recruiting leading researchers in the community to serve as beta testers and role models. Third, we will create tools to easily replicate and extend biomechanics simulations. Containers and cloud computing services allow researchers to capture and share a snapshot of their computing environment, enabling unprecedented fidelity in sharing. We will integrate these technologies into SimTK and provide custom, easy-to-use interfaces to replicate and extend simulation studies. Lastly, we will develop a metadata standard for models and data for the biomechanics community, increasing reusability and discoverability of the rich set of resources shared on SimTK. We will use the new standard on SimTK and fill in the metadata fields automatically using natural language processing and machine learning, minimizing the burden and inaccuracies of manual metadata entry. We will evaluate our success in achieving these aims by tracking the number of assets shared and the frequency they are used as a springboard to new research. These changes will accelerate biomechanics research and provide new tools to increase the reusability and impact of shared resources. By lowering barriers to data sharing in the biosimulation community, SimTK will continue to serve as a model for how to create national infrastructure for scientific subdisciplines.

Public Health Relevance

SimTK is a vibrant hub for the development and sharing of simulation software, data, and models of biological structures and processes. SimTK-based resources are being used to design medical devices and drugs, to generate new diagnostics, to create surgical interventions, and to provide insights into biology. The proposed enhancements to SimTK will accelerate progress in the field by lowering barriers to and standardizing data and model sharing, thus 1) increasing the quantity and also, importantly, the quality of resources that researchers share and 2) enabling others to reproduce and build on the wealth of past biomechanics research studies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Modeling and Analysis of Biological Systems Study Section (MABS)
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Brazhnik, Paul
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Stanford University
Biomedical Engineering
Schools of Medicine
United States
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