NeuroML: Standards and Tools for Multiscale Model Specification and Exchange

NeuroML：多尺度模型规范和交换的标准和工具

• 批准号: 7880643
• 负责人: Sharon Marie Crook
• 金额: $ 29.81万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7880643
• 关键词: Archives; Automobile Driving; Cell model; Cells; Collaborations; Communities; Data; Databases; Development; Dimensions; Discipline; Disease; Documentation; Elements; Ensure; Extensible Markup Language; Feedback; Future; Goals; International; Internet; Ion Channel; Knowledge; Language; Link; Membrane; Metadata; Modeling; Morphology; Nervous system structure; Neurons; Neurosciences; Process; Publications; Publishing; Qi; Research; Research Infrastructure; Research Personnel; Simulate; Structure; Study models; Synapses; Systems Biology; Testing; Trauma; Validation; Work; computational neuroscience; data exchange; data format; data modeling; data sharing; design; interoperability; models and simulation; multi-scale modeling; neural circuit; neuroinformatics; portability; public health relevance; relating to nervous system; tool; tool development

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.

描述（由申请人提供）：与神经科学中的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。 为了联合收割机从多个小组的研究，必须有一个交换模型规范的基础设施，然而，目前使用多种格式的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存档，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标准项目产生的声明性规范被安排成级别，更高的级别添加额外的概念。 第1级处理神经解剖学信息和元数据。 2级允许细胞模型的规范与现实的通道和突触机制分布在其膜上，和3级描述这些细胞在三维网络。 拟议的神经信息学活动的具体目标如下：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）链接，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链接，以及3）在已发表的研究和PI当前研究合作的背景下，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什么问题的理解的最佳方法之一。 研究人员建议继续开发用于计算神经科学的标记语言规范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数据格式。 他们还将继续开发用于验证NeuroML文档的工具，用于文档交换，用于导入/导出NeuroML中的模型规范，以及用于将提交的NeuroML文档文件转换为模拟器脚本或HTML格式。