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

基本信息

  • 批准号:
    8653963
  • 负责人:
  • 金额:
    $ 56.25万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2007
  • 资助国家:
    美国
  • 起止时间:
    2007-09-28 至 2017-03-31
  • 项目状态:
    已结题

项目摘要

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 GM 077138的两年半资助期间,EPA的ComTox计划、邓迪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采用Cell 3D(CC 3D)作为建模平台。CC 3D已成为发育现象和相关疾病的多尺度、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,因为它将Glazier-Graner-Hogeweg(GGH)模型的多细胞功能、SBML兼容的亚细胞生物化学网络以及组织水平现象的连续体和有限元建模开源组合,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级别的有用生物医学模型。由于越来越多的翻译用户的要求,这种竞争性的更新将发展成一种平行的(图形处理器(GPU)、多核和群集)CC 3D 2支持流体流,速度比CC 3D提高了100倍,并且能够运行超大规模模拟(许多cm 3,107-109个细胞,整个胚胎/器官),具有从笔记本电脑到多种并行架构的简单迁移路径(具体目标1)。这很重要,因为CC 3D 2将改变MSMC建模的能力,以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NIH领导的机构间建模和分析小组(IMAG)小组确定的目标:“开发开源、多尺度生物模拟环境,在单处理器和并行计算机上运行,并且. [允许]用户选择模拟详细程度,而无需进一步修改其模拟。“它是创新的,因为它结合了CC 3D开发团队现有的专业知识和D 'Souza团队广泛的GPU和并行化经验,提供了一个强大的并行MSMC环境和第一个基于GPU的GGH方法的实现,以允许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,CC 3D 2将提供一种创新的,快速的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)(具体目标3)和第一个可用于MSMC的共享图形模型定义(具体目标2)。CBMSL将允许研究人员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,为未来的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CC 3D 2的可用性并增加用户采用。

项目成果

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Roshan M D'Souza其他文献

Roshan M D'Souza的其他文献

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{{ truncateString('Roshan M D'Souza', 18)}}的其他基金

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:
    9136441
  • 财政年份:
    2007
  • 资助金额:
    $ 56.25万
  • 项目类别:
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
  • 财政年份:
    2007
  • 资助金额:
    $ 56.25万
  • 项目类别:
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:
    8452175
  • 财政年份:
    2007
  • 资助金额:
    $ 56.25万
  • 项目类别:
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:
    8076579
  • 财政年份:
    2007
  • 资助金额:
    $ 56.25万
  • 项目类别:

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