POSE: PHASE II: Open VT - A Standardized Ecosystem for Virtual Tissue Simulation

POSE：第二阶段：开放 VT - 虚拟组织模拟的标准化生态系统

• 批准号: 2303695
• 负责人: James Glazier
• 金额: $ 150万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-15 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2303695&HistoricalAwards=false
• 关键词: POSE; PHASE; II; Open; VT

Virtual Tissues (VTs) are powerful computer simulations of cell behaviors within tissues andorgans. They are a valuable resource and tool for researchers to delve into the mechanismsdriving both normal and diseased tissue behaviors. Although VTs do not replace traditional wetlabexperiments, they significantly contribute to the exploration and interpretation of existing data.They enable researchers to conduct "virtual" experiments, offering guidance for additionallaboratory and clinical investigations. The combination of VTs with experiments leads to a deepercomprehension of complex biological phenomena and bolsters the progress of scientificunderstanding. VTs play a crucial role in drug and therapy research, as well as in the creation ofMedical Digital Twins for Personalized Medicine. Currently, there is a lack of infrastructure forcollaborative and progressive VT development. This limits their widespread adoption in biologyand medicine. To address this limitation, this project aims to establish an active open-sourcecommunity providing resources and tools—an ecosystem—that fosters collaboration amongresearchers from diverse backgrounds. By facilitating the sharing and application of biomedicaldata and models, this project can transform VT development, accelerating biological and medicalresearch and technological applications. Enhanced sharing and distribution of VTs will positivelyimpact STEM education because VTs present an excellent opportunity to accelerate learning offundamental biological and medical principles in an accessible, appealing, and comprehensiblemanner. By incorporating VTs into educational curricula, the project can expand the reach ofSTEM education and inspire future generations of scientists and researchers. This work bothexpedites scientific discovery and understanding of complex biological systems and alsoadvances American biotechnology and medicine. This project will create OpenVT, an open-source, community-driven collection of resources,standards and tools for expanding the use and adoption of multicellular virtual-tissue (VT)computer simulations of normal and diseased biological tissues. The OpenVT ecosystem willinitially unify and expand two existing widely used open-source platforms for building and runningVT models, CompuCell3D, and PhysiCell. OpenVT will enable sharable, cross-platform modelingtools and shareable model specifications. OpenVT aims to accelerate the understanding ofcomplex biological mechanisms related to tissue development, homeostasis, and disease. Theproject will focus on agent-based modeling (ABM) approaches, where tissues and organs areconstructed using discrete cells, coupled with subcellular network models of signaling, generegulation and metabolism and partial differential equations that simulate the extracellularmovement of oxygen, growth substrates, signaling factors, and therapeutic compounds. Specificaims include: development of shared standards for specification of VT models betweenCompuCell3D and PhysiCell, creation of cell-type description libraries, standardization of initialconditions, and description of model outputs. These standards will then be used to define theneeded APIs that allow the interconnection and reuse of models and software components acrossthe two platforms, while also providing a concrete technical roadmap to support the integration ofadditional open source ABM VT frameworks in the future. This approach allows for the integrationof subcellular, cell-level, and tissue-level phenomena, providing explanatory power and enablinghigh-precision virtual experiments. The project will support the integration of other VT frameworksand the creation of educational and distribution facilities to enable their widespread adoption andextension of OpenVT. The OpenVT ecosystem aligns with successful community-driven initiativesin scientific software development, such as the Systems Biology Markup Language (SBML)project. It aims to foster collaboration, establish standards for model inputs and outputs, andprovide user support and training. By transitioning to an open-source ecosystem, the project aimsto reduce duplication of effort, promote software and modle sharing, and democratize access tomodeling capabilities. Project outcomes will be available at OpenVT.org.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

虚拟组织（VTS）是对组织内细胞行为的强大计算机模拟。它们是研究人员探究正常组织行为和脱离组织行为的机制的宝贵资源和工具。尽管VT不能取代传统的Wetlabexperiments，但它们有助于探索和解释现有数据。它们使研究人员能够进行“虚拟”实验，从而为额外的代理和临床研究提供指导。 VT与实验的结合导致对复杂的生物学现象的更深入的理解，并使科学理解的进步变得更深入。 VTS在药物和治疗研究中以及创建用于个性化医学的医学数字双胞胎中起着至关重要的作用。目前，缺乏基础设施伪造和进步的VT开发。这限制了他们在生物学和医学领域的广泛采用。为了应对这一限制，该项目旨在建立一个积极的开放式开放式社区，以提供资源和工具（一个生态系统），从而促进了来自潜水员背景的搜索者之间的协作。通过支持生物医学数据和模型的共享和应用，该项目可以改变VT开发，加速生物学和医学研究以及技术应用。 VTS的共享和分配增强将对STEM教育产生积极影响，因为VT是一个极好的加速机会。以一种可访问，出现和全面的方式学习未来的生物学和医学原理。通过将VT纳入教育课程，该项目可以扩大STEM教育的影响力并激发后代的科学家和研究人员。这项工作大比喻的科学发现和对复杂生物系统的理解，并推进了美国的生物技术和医学。该项目将创建OpenVT，这是一个开源，由社区驱动的资源，标准和工具集合，用于扩大和采用正常生物组织和否定生物组织的多细胞虚拟组织（VT）计算机模拟。 OpenVT生态系统将在构建和RuntionVT模型，Compucell3D和Physicell上统一并扩展两个现有的广泛使用的开源平台。 OpenVT将启用可共享的跨平台建模工具和可共享模型规范。 OpenVT旨在加快与组织发育，稳态和疾病有关的复杂生物学机制的理解。该项目将重点关注基于代理的建模（ABM）方法，其中组织和器官是使用离散细胞构建的，并与信号传导，结构调节和代谢的亚细胞网络模型以及模拟氧气外运动，生长底物，信号传导因素和治疗化合物的细胞外运动。特定aims包括：开发用于VT模型的共享标准botweencompucell3d和Physicell，创建细胞类型的描述库，初始条件的标准化以及模型输出的描述。然后，这些标准将用于定义以下API，以允许在两个平台上互连和重复使用模型和软件组件，同时还提供了具体的技术路线图，以支持将来其他开源ABM VT框架集成。这种方法允许将亚细胞，细胞水平和组织级现象整合起来，从而提供剥夺能力并实现高精度虚拟实验。该项目将支持其他VT框架的集成，并建立教育和分销设施，以使其广泛采用和扩展OpenVT。 OpenVT生态系统与在科学软件开发中成功的社区驱动计划一致，例如Systems Biology标记语言（SBML）项目。它旨在培养合作，建立模型输入和输出的标准，并提供用户支持和培训。通过过渡到开源生态系统，该项目Aimsto减少了努力，促进软件和Modle共享的重复，并使访问中心的能力民主化。项目成果将在OpenVT.org上获得。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响评论标准，被认为是值得的支持。