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）：与神经科学中结构和功能相关的问题的复杂性要求将多个小组的研究组合在一起。 为了结合多个组的研究，必须有一个基础架构来交换模型规格。但是，当前使用多种格式用于编码模型信息已阻碍模型交换。 NeuroMl是一种可扩展的标记语言（XML）规范，以促进神经科学中的数据归档，数据和模型交换，数据库创建和模型出版物。 Neuroml项目的目标之一是为模型规范制定标准，该标准将允许更大的模拟器互动性和模型交换。 神经标准项目产生的声明性规范被整合到水平上，更高的级别增加了额外的概念。 1级处理神经解剖信息和元数据。 级别2允许规定具有逼真的通道和分布在其膜上的突触机制的细胞模型，并且第3级描述了这些细胞的网络在三个维度上。 所提出的神经信息活动的具体目的如下：1）将扩展神经元标准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）联系起来，以创建XML的XML规范，以在神经科学中为其他级别的神经级别的链接，2）与其他级别的神经级别的链接，2） 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神经元的使用示例，并测试架构设计，工具以及与创世纪，神经元和其他适当的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问题的最佳方法之一。 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，即NeuroMl，该规范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神经文档，文档交换，导入/导出Neuroml中的模型规范的工具，以及将提交的Neuroml文档文件转换为模拟器脚本或HTML格式。