SimTK: An Ecosystem for Data and Model Sharing in the Biomechanics Community

基于物理的模拟为理解生物的形式和功能提供了一个强大的框架。他们 协调异构实验数据与现实世界的物理约束，帮助研究人员 了解生物系统，因为他们工程新药，新的诊断，医疗设备和外科手术， 干预措施。新传感器和模拟工具的兴起正在产生越来越多的数据，但这 数据往往无法获取，妨碍了再利用，限制了科学进步。2005年，我们推出了SimTK， 网站开发和共享生物模拟工具，模型和数据，以解决这些问题。SimTK现在 支持全球62，000多名研究人员和950多个项目。成员使用它来满足他们的赠款的数据共享 责任;尝试新的协作方式;围绕数据集建立社区， 工具.然而，挑战仍然存在：由于时间的限制，许多研究人员仍然没有分享他们的数字资产。 需要准备、记录和维护这些资产，而且由于SimTK托管了越来越多的各种 除了数字资产之外，该网站现在还面临着使这些资产可重复使用的挑战。因此，在本发明中， 我们提出了一个扩展SimTK的计划，并实施了新的解决方案，以促进科学数据的共享和重用。 首先，我们将保持SimTK建立的可靠、用户友好的基础，继续提供 优秀的支持我们的成员期望和支持网站的现有功能的共享和建设 社区.第二，我们将实施各种方法，在全球范围内建立一种模型和数据共享的文化， 生物力学社区我们将鼓励研究人员养成新的习惯，使分享成为他们生活的一部分。 工作流程，通过启用他们使用的软件和系统自动将模型和数据上传到SimTK 通过应用程序编程接口（API），并通过招募社区中的领先研究人员来服务 作为beta测试者和榜样第三，我们将创造工具，轻松复制和扩展生物力学 模拟容器和云计算服务允许研究人员捕获和共享 他们的计算环境，实现了前所未有的共享保真度。我们将整合这些技术 并提供自定义、易于使用的界面来复制和扩展模拟研究。最后我们 将为生物力学社区开发模型和数据的元数据标准，提高可重用性 以及SimTK上共享的丰富资源集的可扩展性。我们将在SimTK上使用新标准， 使用自然语言处理和机器学习自动填写元数据字段， 手动元数据输入的负担和不准确性。我们将评估我们在实现这些目标方面的成就 通过跟踪共享资产的数量和使用频率，将其作为新研究的跳板。 这些变化将加速生物力学研究，并提供新的工具，以增加可重用性， 共享资源的影响。通过降低生物模拟社区中数据共享的障碍，SimTK将 继续作为如何为科学分支学科建立国家基础设施的典范。

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.