Development and Improvement of Tissue Simulation Toolkit

组织模拟工具包的开发和改进

• 批准号: 7234925
• 负责人: James Alexander Glazier
• 金额: $ 53万
• 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 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7234925
• 关键词: Behavior; Biochemical; Biological; Biological Models; Biological Process; Biomedical Research; Blood Vessels; Cell Communication; Cell Count; Cell Polarity; Cell Shape; Cell model; Cell physiology; Cells; Class; Code; Commit; Communities; Computer software; Computers; Critiques; Data Analyses; Databases; Depth; Development; Dictyostelium discoideum; Diffusion; Disease; Documentation; Educational workshop; Embryonic Development; Ensure; Environment; Evolution; Future; Goals; Graduate Education; Home environment; Human; Imagery; Immune system; Individual; Kinetics; Language; Language Development; Lead; Letters; Link; Linux; Liquid substance; Mechanics; Metabolic; Methodology; Methods; Microscope; Modeling; Monitor; Numbers; Organ; Organism; Outcome; Pathology; Play; Procedures; Property; Publications; Reaction; Reporting; Research; Research Personnel; Role; Running; Sampling; Scientist; Signal Transduction; Software Tools; Solid; Source Code; Specialist; Standards of Weights and Measures; Structure; Support System; Surveys; Systems Biology; Techniques; Testing; Tissues; Training; United States National Institutes of Health; Validation; Work; Wound Healing; Writing; base; biological research; cell behavior; design; graphical user interface; improved; interoperability; large scale simulation; life history; model development; models and simulation; multi-scale modeling; open source; parallel computer; parallel computing; programs; research study; response; simulation; therapy development; tool; tumor growth; usability

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，即组织模拟环境（TSE），用于使用细胞波茨模型对组织和器官的结构和行为进行基于细胞的建模（CPM）形式主义。虽然世界各地的研究小组已经使用 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，但目前没有开源包支持此类模型。我们的具体目标是 TSE 应该提供与其他 CPM 模拟相当或更好的建模能力，并且可供广泛的生物建模者和实验者群体使用并对其有吸引力。为了实现这一目标，我们将提供高度可扩展的核心模拟引擎、大量经过验证的样本生物模型、具有可视化功能的灵活直观的图形用户界面、广泛的文档以及许多描述其他 CPM 模拟中未包含的生物过程的模块。此外，我们将提供用户培训研讨会并持续进行用户需求调查。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，以确保其以响应用户的方式快速可靠地开发。相关性：胚胎发育、伤口愈合和疾病过程中细胞相互作用的模拟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，提出实验建议，预测实验结果并导致对基本生物机制的更深入理解，从而加快对疾病的了解和治疗策略的制定。