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将来自多个学科的多个小组的研究结合起来。 为了结合多个小组的研究，必须有一个用于交换模型规范的基础设施；然而，当前使用多种格式来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，旨在促进神经科学领域的数据归档、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标准，以实现更好的模拟器互操作性和模型交换。 NeuroML 标准项目生成的声明性规范分为多个级别，更高的级别添加了额外的概念。 第 1 级处理神经解剖信息和元数据。 第 2 级允许指定具有分布在其膜上的真实通道和突触机制的细胞模型，第 3 级描述这些细胞在三个维度上的网络。 拟议的神经信息学活动的具体目标如下：1）NeuroML 标准将扩展以适应生物分子相互作用模型，并将链接到系统生物学标记语言（SBML），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 标准和相关工具将扩展并链接到其他神经信息学工作，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 NeuroML 的使用示例，并测试架构设计、工具以及与 GENESIS、NEURON 和其他适当模型模拟平台的兼容性。 公共卫生相关性：建立神经元和神经回路的工作模型是进一步了解神经系统如何工作以及神经创伤或疾病后出现问题的最佳方法之一。 研究人员建议继续开发计算神经科学标记语言规范 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、NeuroML 模型规范导入/导出以及将提交的 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.