Database for the Analysis of Neuronal Structure and Function

摘要DBI 9808738；雅各布斯，格温；蒙大拿州立大学神经系统是在先前的美国国家科学基金会资助下开发的一个原型数据库，其中包含关于神经元的解剖和功能属性的信息。NeuroSys还包含有关神经元之间测量和假设关系的信息。此外，该数据库环境还集成了一个高级可视化程序，用于组合活动模式的动态合成和动画制作。最后，一个先进的神经模拟程序也已经集成到这个环境中。通过使用这些先进的查询和分析工具，现在可以制定查询来预测动物神经系统内多个处理阶段的大型神经元集合的动态活动模式。这些特点使数据库的效用远远超过复杂的数据储存库，并为提出与神经计算、可塑性和发育有关的假设提供了一种使能工具。这项工作的总体目标是扩展该原型系统的能力、可移植性和通用性，并将该系统分发给神经科学界所有感兴趣的研究人员。具体目标如下：图形用户界面的功能及其与数据分析程序的链接将通过修改体系结构而得到加强，以更有效地适应分布式数据和新的软件工具，并允许用户进行复杂的查询，而不影响其他用户的数据。-数据采集、分析和查询工具将得到增强，以适应几种新的数据类型，包括a)基于体素的单个神经元和/或物体的表示，作为来自共焦显微镜图像的密度云；b)从单电极和多电极记录产生的时间序列数据；以及c)表面渲染和体积渲染结构，来自从切片组织样本追踪的物体的显微镜图像。-将在数据库/工作空间环境和三个流行的神经建模程序之间建立链接。-将采用新的软件工具，以方便其他用户配置系统。这些工具将包括一个生成和定制查询界面/图形用户界面的程序，以及一个根据一组用户定义的输入生成数据库表的程序--用户基础将扩展到一般神经科学研究社区。作为这一进程的一部分，该系统将通过测试版测试程序进行验证，将提高工具在几个硬件和软件平台上的稳定性和可移植性，并将开发一个界面，用于基于网络的访问和数据输入。-蒙大拿州立大学目前的生物信息学多学科培训环境将通过基于项目各个方面的指导和独立研究项目得到支持和扩展。然后，将开发一套课程模块，通过基于Java的网络接口连接到数据库和工具，供课堂使用。这些单元将在当地的许多课程中使用，并将通过网络向公众提供。这个项目将由两组神经科学和计算机科学研究人员协调进行：一组在密歇根州立大学，另一组在加州大学圣迭戈分校。该项目是NPACI神经科学推力领域的核心组成部分，将利用圣地亚哥中心丰富的技术专长和计算机资源。

AbstractDBI 9808738; Jacobs, Gwen; Montana State UniversityNeuroSys is a prototype database developed under prior NSF funding which contains information about the anatomy and functional attributes of neurons. NeuroSys also contains information about measured and hypothetical relations between neurons. In addition an advanced visualization program for dynamic synthesis and animation of ensemble activity patterns has been integrated into this database environment. Finally, an advanced neural simulation program has also been integrated with this environment. Through the use of these advanced query and analysis tools, it is now possible to formulate queries which predict dynamic activity patterns of large neuronal ensembles across multiple processing stages within an animal's nervous system. These features elevate the utility of the database far beyond that of a sophisticated data repository, and provide an enabling tool for the formulation of hypotheses related to neural computation, plasticity and development. The general goals of this work are to extend the capabilities, transportability and general utility of this prototype system, and to distribute this system to all interested researchers in the neuroscience community. Specific aims are as follows:Ñ The functionality of the graphical user interface and its links to data analysis programs will be enhanced by modification of the architecture to accommodate distributed data and new software tools more effectively, and to allow users to conduct complex queries without affecting the data of other users. Ñ The data acquisition, analysis and query tools will be enhanced to accommodate several new data types, including a) Voxel-based representations of individual neurons and/or objects as density clouds derived from confocal microscope images, b) time-series data generated from single and multi-electrode recordings, and c) surface-rendered and vol-ume-rendered structures derived from microscope images of objects traced from sec-tioned tissue samples. Ñ A link will be created between the database/workspace environment and three popular neural modeling programs.Ñ New software tools will be implemented to facilitate the configuration of the system for other users. Those tools will include a program to generate and customize the query interface/GUI, and a program to generate database tables from a set of user-defined inputsÑ The user base will be extended to the general neuroscience research community. As part of this process, the system will be validated through a beta test program, the stabil-ity and transportability of the tools across several hardware and software platforms will be increased, and an interface will be developed for web-based access and data entry. Ñ The current multi-disciplinary training environment for bioinformatics at Montana State University will be supported and extended, through directed and independent research projects based on aspects of the project. A set of coursework modules will then beÑ developed for classroom use via a Java-based web interface to the database and tools. These modules will be used in a number of courses locally, and will be made available to the general public via the web.This project will be carried out as a coordinated effort between two sets of neuroscience and computer science researchers: one group at MSU and the other group at UCSD. This project is a core component in the NPACI Neuroscience Thrust Area, and will leverage on a wealth of technical expertise and computer resources at the San Diego center.