Development and Improvement of Tissue Simulation Toolkit
组织模拟工具包的开发和改进
基本信息
- 批准号:7502004
- 负责人:
- 金额:$ 51.32万
- 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 2010-08-31
- 项目状态:已结题
- 来源:
- 关键词:BehaviorBiochemicalBiologicalBiological ModelsBiological ProcessBiomedical ResearchBlood VesselsCell CommunicationCell CountCell PolarityCell ShapeCell modelCell physiologyCellsClassCodeCommitCommunitiesComputer softwareComputersCritiquesData AnalysesDatabasesDepthDevelopmentDictyostelium discoideumDiffusionDiseaseDocumentationEducational workshopEmbryonic DevelopmentEnsureEnvironmentEvolutionFutureGoalsGraduate EducationHome environmentHumanImageryImmune systemIndividualKineticsLanguageLanguage DevelopmentLeadLettersLinkLinuxLiquid substanceMechanicsMetabolicMethodologyMethodsMicroscopeModelingMonitorNumbersOrganOrganismOutcomePathologyPlayProceduresPropertyPublicationsReactionReportingResearchResearch PersonnelRoleRunningSamplingScientistSignal TransductionSoftware ToolsSolidSource CodeSpecialistStandards of Weights and MeasuresStructureSupport SystemSurveysSystems BiologyTechniquesTestingTissuesTrainingUnited States National Institutes of HealthValidationWorkWound HealingWritingbasebiological researchcell behaviordesigngraphical user interfaceimprovedinteroperabilitylarge scale simulationlife historymodel developmentmodels and simulationmulti-scale modelingopen sourceparallel computerparallel computingprogramsresearch studyresponsesimulationtherapy developmenttooltumor growthusability
项目摘要
DESCRIPTION (provided by applicant): Project Summary: We propose to develop an open-source modeling environment, the Tissue-Simulation Environment (TSE), for the cell-based modeling of the structure and behavior of tissues and organs using the Cellular Potts Model (CPM) formalism. While groups worldwide have used the CPM methods to model biomedical phenomena, including vascular development, tumor growth, wound healing and the immune system, no open-source package currently supports this class of model. Our Specific Aim is that the TSE should provide modeling capability comparable to or better than other CPM simulations and be usable by and attractive to a broad community of biomodelers and experimentalists. To accomplish this aim we will provide a highly expandable core simulation engine, numerous validated sample biological models, a flexible and intuitive graphical user interface with visualization capability, extensive documentation and a number of modules describing biological processes not included in other CPM simulations. In addition we will provide user-training workshops and conduct ongoing user-need surveys. In response to the NIH Roadmap's call for interoperability and multiscale simulations, the TSE will also provide connectivity to other major subcellular and tissue-level software packages through a program of markup- language development and support. The TSE will also provide a mechanism to collect, validate and release user-submitted modules, models, bug reports and fixes to ensure that it develops rapidly and reliably in a way responsive to its users. Relevance: Simulations of cell interactions during embryonic development, wound healing, and disease can play an important role in experimental biomedical studies, help with the interpretation of experimental results, suggest experiments, predict experimental outcomes and lead to deeper understanding of fundamental biological mechanisms, thus expediting the understanding of diseases and the development of treatment strategies.
描述(由申请人提供):项目摘要:我们建议开发一个开源建模环境,组织模拟环境(TSE),用于使用细胞Potts模型(CPM)形式主义对组织和器官的结构和行为进行基于细胞的建模。虽然世界各地的组织都使用CPM方法来模拟生物医学现象,包括血管发育,肿瘤生长,伤口愈合和免疫系统,但目前没有开源软件包支持这类模型。我们的具体目标是,TSE应提供建模能力相媲美或优于其他CPM模拟,并可用于和吸引广泛的社区biomodelers和实验。为了实现这一目标,我们将提供一个高度可扩展的核心模拟引擎,许多经过验证的样本生物模型,一个灵活和直观的图形用户界面与可视化功能,广泛的文档和一些模块描述生物过程不包括在其他CPM模拟。此外,我们将提供用户培训讲习班,并进行持续的用户需求调查。为了响应NIH路线图对互操作性和多尺度模拟的呼吁,TSE还将通过标记语言开发和支持计划提供与其他主要亚细胞和组织级软件包的连接。TSE还将提供一种机制来收集、验证和发布用户提交的模块、模型、错误报告和修复程序,以确保其以响应用户的方式快速可靠地开发。相关性:模拟胚胎发育、伤口愈合和疾病过程中的细胞相互作用可以在实验生物医学研究中发挥重要作用,有助于解释实验结果,建议实验,预测实验结果,并加深对基本生物机制的理解,从而加快对疾病的理解和治疗策略的制定。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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James Alexander Glazier其他文献
James Alexander Glazier的其他文献
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{{ truncateString('James Alexander Glazier', 18)}}的其他基金
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$ 51.32万 - 项目类别:
Development and Improvement of Tissue Simulation Toolkit
组织模拟工具包的开发和改进
- 批准号:
7681269 - 财政年份:2007
- 资助金额:
$ 51.32万 - 项目类别:
Development and Improvement of Tissue Simulation Toolkit
组织模拟工具包的开发和改进
- 批准号:
7234925 - 财政年份:2007
- 资助金额:
$ 51.32万 - 项目类别:
MSM - Multiscale Studies of Segmentation in Vertebrate *
MSM - 脊椎动物分割的多尺度研究*
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7283086 - 财政年份:2005
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$ 51.32万 - 项目类别:
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8139095 - 财政年份:2005
- 资助金额:
$ 51.32万 - 项目类别:
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$ 51.32万 - 项目类别:
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- 批准号:
8728259 - 财政年份:2005
- 资助金额:
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