NeuroML: Standards and Tools for Multiscale Model Specification and Exchange

描述（由申请人提供）：神经科学中与结构和功能相关的问题的复杂性要求来自多个学科的多个小组的研究相结合。为了将来自多个小组的研究结合起来，必须有一个交换模型规范的基础设施；然而，目前使用多种格式编码模型信息阻碍了模型交换。NeuroML是一种可扩展标记语言（XML）规范，旨在促进神经科学中的数据归档、数据和模型交换、数据库创建和模型发布。NeuroML项目的目标之一是开发模型规范的标准，这将允许更大的模拟器互操作性和模型交换。由NeuroML标准项目生成的声明性规范被安排为级别，更高的级别添加额外的概念。第一级处理神经解剖学信息和元数据。第2级允许使用分布在细胞膜上的真实通道和突触机制规范细胞模型，第3级以三维方式描述这些细胞的网络。拟议的神经信息学活动的具体目的如下：1) NeuroML标准将被扩展，以适应生物分子相互作用的模型，并将与系统生物学标记语言（SBML）相关联，以便为神经科学中的多尺度模型创建XML规范；2)所有级别的NeuroML标准和相关工具将被扩展并与其他神经信息学工作相关联；3)在已发表的研究和PI当前的研究合作的背景下，建模研究将用于生成使用NeuroML的示例，并测试模式设计、工具以及与GENESIS、NEURON和其他适当模型仿真平台的兼容性。公共卫生相关性：建立神经元和神经回路的工作模型是加深我们对神经系统如何工作以及神经创伤或疾病后出现问题的理解的最佳途径之一。研究人员建议继续开发计算神经科学的标记语言规范，即NeuroML，它将作为许多应用程序的通用数据格式，包括模拟模型所必需的应用程序。他们还将继续开发用于验证NeuroML文档、文档交换、在NeuroML中导入/导出模型规范以及将提交的NeuroML文档文件转换为模拟器脚本或HTML格式的工具。

DESCRIPTION (provided by applicant): The complexity of problems associated with structure and function in neuroscience requires that research from multiple groups across many disciplines be combined. In order to combine research from multiple groups, there must be an infrastructure for exchanging model specifications; however, the current use of multiple formats for encoding model information has hampered model exchange. NeuroML is an eXtensible Markup Language (XML) specification that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the NeuroML project is to develop standards for model specification that will allow for greater simulator interoperability and model exchange. The declarative specifications produced by the NeuroML standards project are arranged into levels, with higher levels adding extra concepts. Level 1 deals with neuroanatomical information and metadata. Level 2 allows for specification of cell models with realistic channel and synaptic mechanisms distributed on their membranes, and Level 3 describes networks of these cells in three dimensions. The specific aims of the proposed neuroinformatic activities are as follows: 1) the NeuroML standards will be extended to accommodate models of biomolecular interactions and will be linked to the Systems Biology Markup Language (SBML) in order to create an XML specification for multiscale models in neuroscience, 2) all levels of the NeuroML standards and associated tools will be extended and linked to other neuroinformatic efforts, and 3) within the context of both published studies and the PI's current research collaborations, modeling studies will be used to generate examples of the use of NeuroML and to test the schema design, tools, and compatibility with GENESIS, NEURON, and other appropriate model simulation platforms. PUBLIC HEALTH RELEVANCE: Building working models of neurons and neural circuits is one of the best ways of furthering our understanding of how the nervous system works and what goes wrong following neural trauma or disease. The investigators propose to continue the development of a markup language specification for computational neuroscience, NeuroML, which will serve as a common data format for many applications including those necessary for simulating models. They will also continue their development of tools for validation of NeuroML documents, for document exchange, for import/export of model specifications in NeuroML, and for conversion of submitted NeuroML document files into simulator scripts or HTML format.