Development and Improvement of Tissue Simulation Toolkit

描述(由申请人提供)：项目摘要：我们建议开发一个开源的建模环境，组织模拟环境(TSE)，用于使用细胞Potts模型(CPM)形式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，但目前还没有开放源码包支持这类模型。我们的具体目标是，TSE应该提供与其他CPM模拟相媲美或更好的建模能力，并可供广大生物模型师和实验者使用并吸引他们。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、大量经过验证的生物样本模型、具有可视化能力的灵活直观的图形用户界面、广泛的文档和许多描述其他CPM模拟中未包括的生物过程的模块。此外，我们还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别的软件包的连接。东京证券交易所还将提供一种机制，以收集、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而可靠地开发。相关性：对胚胎发育、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，帮助解释实验结果，建议实验，预测实验结果，并导致对基本生物学机制的更深入理解，从而加速对疾病的理解和治疗策略的制定。

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.