Simtk.org: A Resource to Enable Collaboration & Reproducibility of Biosimulations

基于物理的模拟为理解生物学提供了一个强大的框架 形式和功能。模拟帮助生物医学研究人员了解物理 对生物系统的限制，因为他们设计了新的药物，新的诊断， 合成组织、医疗器械和外科干预。不幸的是，在 个别调查人员发布他们的工作、软件、基础模型和 模拟结果通常是不可访问的，这限制了进展。2005年，我们推出了 开发和共享生物模拟工具、模型和数据的网站Simtk.org， 解决这个问题。Simtk.org现在为全球超过23,000名研究人员提供支持 600个项目。成员使用Simtk.org围绕他们的社区开发和构建社区 模拟工具，履行其授权的数据共享责任，并创建新的 协作的类型。因此，Simtk.org是国家基础设施如何 是为科学分支学科而创建的。我们的用户帮助我们确定了关键 进一步提高我们影响力的机会：促进忠实地复制 调查人员的模拟结果，捕捉模拟研究的全部细微差别， 并为研究人员提供访问他们的数据、模型和 软件。因此，我们提出了一个扩展Simtk.org的计划，并建立了新的科学方法 数据共享。首先，我们将创建原型工具，使其他人能够轻松复制 并扩展生物模拟结果。虚拟机和云计算服务支持 研究人员捕获并共享其完整计算环境的快照， 实现前所未有的共享保真度。我们将探索如何使用这些 在Simtk.org上复制生物模拟研究。第二，我们将戏剧性地 增加以模拟为基础的科学出版物与其支持的整合 数据。与生物模拟出版物的主要期刊的编辑合作，我们将 扩展Simtk.org以将已发表的文章直接链接到所需的资源 理解、检查和复制他们的结果。三是提高健壮性 以及Simtk.org的可用性，这样依赖于该站点的不断增长的社区可以 继续对资源的可获得性和稳定性充满信心地工作。 第四，我们将开发利用社交网络来激励和奖励的技术 积极参与Simtk.org社区的研究人员。Simtk.org是一个“中间-- 社交网络规模“具有特定焦点和目的的关键优势。因此， 它为如何建立共享和社区的科学资源提供了一个模式 大楼。拟议的对Simtk.org的增强将显著加快研究 并为科学研究人员之间的互动提供了一种新的模型。

Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, new diagnostics, synthetic tissues, medical devices, and surgical interventions. Unfortunately, after individual investigators publish their work, the software, underlying models and simulation results are often inaccessible, limiting progress. In 2005, we launched Simtk.org, a website to develop and share biosimulation tools, models, and data, to address this issue. Simtk.org now supports over 23,000 researchers globally and over 600 projects. Members use Simtk.org to develop and build communities around their simulation tools, fulfill the data sharing responsibilities for their grants, and create new types of collaborations. Thus, Simtk.org is a model for how national infrastructure can be created for scientific subdisciplines. Our users have helped us identify key opportunities to further increase our impact: facilitating the faithful reproduction of simulation results across investigators, capturing the full nuances of a simulation study, and creating incentives for researchers to provide access to their data, models and software. Thus, we propose a plan to extend Simtk.org and build new ways for scientific data sharing. First, we will create prototype tools that enable others to easily reproduce and extend biosimulation results. Virtual machines and cloud computing services allow researchers to capture and share a snapshot of their complete computing environment, enabling unprecedented fidelity in sharing. We will explore how these could be used within Simtk.org to reproduce biosimulation studies. Second, we will dramatically increase the integration of simulation-based scientific publications with their supporting data. Working with the editors of major journals for biosimulation publications, we will extend Simtk.org to directly link published articles to the resources needed to understand, examine and replicate their results. Third, we will improve the robustness and usability of Simtk.org, so that the growing community who rely on the site can continue their work with full confidence in the availability and stability of the resource. Fourth, we will develop techniques using social networking to motivate and reward researchers who actively participate in the Simtk.org community. Simtk.org is a "middle- sized social network" with the key advantage of a specific focus and purpose. As such, it serves as a model for how to build a scientific resource for sharing and community building. The proposed enhancements to Simtk.org will significantly accelerate research in biosimulation and offer a new model for interactions between scientific researchers.