Competitive Renewal of Development, Improvement and Extension of the Tissue Simu

组织模拟的开发、改进和扩展的竞争性更新

• 批准号: 8281441
• 负责人: Roshan M D'Souza
• 金额: $ 56.97万
• 依托单位: TRUSTEES OF INDIANA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-28 至 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8281441
• 关键词: Address; Adopted; Adoption; Age related macular degeneration; Architecture; Basic Science; Binding; Biochemical; Biological; Biology; Bone Regeneration; Cell model; Cells; Clinical; Clinical Research; Code; Communities; Development; Diffusion; Disease; Disease Progression; Documentation; Educational workshop; Elements; Embryo; Environment; Event; Evolution; Funding; Future; Generations; Goals; Individual; Institution; Kinetics; Language; Letters; Libraries; Liquid substance; Mentorship; Methodology; Modeling; Nature; Neoplasm Metastasis; Neoplasms in Vascular Tissue; Operating System; Organ; Organ Size; Process; Publishing; Pythons; Radiation Oncology; Reaction; Research; Research Personnel; Running; Site; Source; Speed; Standardization; Structure; Suggestion; Techniques; Tissue Engineering; Tissue Model; Tissues; Toxicology; Training; United States National Institutes of Health; Validation; Zebrafish; base; cell behavior; cell type; clinically relevant; computer cluster; distributed memory; experience; fluid flow; graphical user interface; improved; innovation; laptop; large scale simulation; migration; model design; model development; movie; multi-scale modeling; novel; oncology; open source; outreach; parallel computer; parallel computing; programs; scripting interface; simulation; tool; tumor growth; usability

DESCRIPTION (provided by applicant): During two-and-a-half years of funding under NIH GM077138, the EPA's ComTox program, the Dundee computational oncology effort and an increasing number of developmental biologists and tissue engineers have adopted CompuCell3D (CC3D) as a modeling platform. CC3D has become the most widely accepted standard for multi-scale, multi-cell (MSMC) simulations of developmental phenomena and related diseases, with more than 100 trained users, because its open-source combination of the multi-cell capabilities of the Glazier-Graner-Hogeweg (GGH) model, the SBML-compatible subcellular biochemical networks, and continuum and finite-element modeling of tissue-level phenomena, sophisticated user interfaces and scripting capabilities allow rapid construction of useful biomedical models with tunable levels of modeling detail. Motivated by the requests of our increasing number of translational users, this competing renewal will develop a parallel (Graphical Processing Unit (GPU), multi-core and cluster) CC3D2 with fluid-flow support providing up to a hundred-fold increase in speed over CC3D plus the ability to run very large-scale simulations (many cm3, 107-109 cell, whole embryo/organ) with a simple migration path from laptop to diverse parallel architectures (Specific Aim 1). It is significant, because CC3D2 will transform the power of MSMC modeling to allow the development of the detailed, verifiable models required for future clinical-research applications, achieving the goal identified by the NIH-led Interagency Modeling and Analysis Group (IMAG) group: "the development of open source, multi-scale biological simulation environments which run both on single processors and parallel computers and which ..., [permit] users to select the level of simulation detail without further modifying their simulations." It is innovative because it combines the existing expertise of the CC3D development team and the extensive GPU and parallelization experience of the D'Souza group to provide a robust parallel MSMC environment and the first GPU-based implementation of the GGH methodology to allow simulations which were formerly unachievable. As requested by our clinical and biomedical users, CC3D2 will provide an innovative, fast and biologically- intuitive approach to model design, with a novel Cell Behavior Model Specification Language (CBMSL) (Specific Aim 3) and the first sharable graphical model definition available for MSMC (Specific Aim 2). CBMSL will allow researchers to focus on biology rather than computational details and greatly facilitate model cross-validation and sharing, providing an important use-case for future MSMC model-description standardization efforts. Graphical workflow control and enhanced user support and documentation (Specific Aim 4) will further improve CC3D2 usability and increase user adoption.

描述(由申请人提供)：在NIH GM077138、EPA的ComTox计划、Dundee计算肿瘤学工作以及越来越多的发育生物学家和组织工程师的两年半资助期间，已采用CompuCell3D(CC3D)作为建模平台。CC3D已成为对发育现象和相关疾病进行多尺度、多细胞(MSMC)模拟的最广泛接受的标准，拥有100多名训练有素的用户，因为其开源组合Glazier-Graner-Hogeweg(GGH)模型的多细胞功能、兼容SBML的亚细胞生化网络、组织水平现象的连续和有限元建模、复杂的用户界面和脚本功能允许快速构建具有可调建模细节水平的有用生物医学模型。在我们越来越多的翻译用户的请求的激励下，这一竞争更新将开发具有流体支持的并行(图形处理单元(GPU)、多核和集群)CC3D2，提供比CC3D高达100倍的速度，并且能够运行非常大规模的模拟(许多cm3、107-109细胞、整个胚胎/器官)，并且具有从笔记本电脑到不同并行体系结构的简单迁移路径(特定目标1)。它意义重大，因为CC3D2将改变MSMC建模的力量，允许开发未来临床研究应用所需的详细、可验证的模型，实现由NIH领导的跨机构建模和分析小组(IMAG)确定的目标：“开发在单处理器和并行计算机上运行的开源、多尺度生物模拟环境……[允许]用户在不进一步修改他们的模拟的情况下选择模拟细节的水平。”它是创新的，因为它结合了CC3D开发团队现有的专业知识和D‘Souza团队丰富的GPU和并行化经验，提供了强大的并行MSMC环境和第一个基于GPU的GGH方法实施，从而实现了以前无法实现的模拟。根据我们的临床和生物医学用户的要求，CC3D2将提供一种创新、快速和生物直观的模型设计方法，具有新颖的细胞行为模型规范语言(CBMSL)(特定目标3)和首个可供MSMC共享的图形模型定义(特定目标2)。CBMSL将使研究人员能够专注于生物学而不是计算细节，并极大地促进模型交叉验证和共享，为未来MSMC模型描述标准化工作提供重要的用例。图形化的工作流程控制和增强的用户支持和文档(具体目标4)将进一步提高CC3D2的可用性并增加用户采用率。