A Portable Client-Server Data Management System for the Comparative Analysis of Proteins

该项目将开发一个数据管理系统，以支持对相关蛋白质组感兴趣的分子生物学家的各种重要数据。该系统将由圣地亚哥超级计算机中心（SDSC）分发，作为现有生物数据资源的一部分，除其他外，支持蛋白激酶家族的酶数据（http://www.sdsc.edu/kinases）和使用x射线晶体学获得的时间三维结构数据。该系统将允许整合序列同源性、结构同源性、功能和疾病的查询，这是当前一代分子生物学资源无法实现的。总体目标是为社区提供一个非专有的系统，该系统高效、可扩展，并且对于分子生物学家来说，可以简单地用于加载他们自己的数据。这些数据可以是现有来源提供的数据子集和/或他们自己的私有数据。该系统将用Java（或具有同等功能的语言）进行编码，将在本地计算机上运行，或者在使用局域网或Internet的客户机-服务器环境中运行。具体的成果有：(1)紧凑的二进制数据存储，面向对象的大分子特征的内存表示，以及适用于分析蛋白质中发现的比较特征的查询方法。这是已经在软件WPDB （http://www.sdsc.edu/CCMS/Packages/wpdb.html）和MOOSE （http://www.sdsc.edu/moose）中找到的技术的扩展。（二）客户端-服务器环境，超越目前万维网提供的无状态访问。（III）将用c++编写的现有方法移植到Java中，并创建新方法，提供用于分子生物学的applet库。（IV）用Java编写的专门用于分子生物学的低级图形库。(V)分子生物学查看器（即特定领域的浏览器、编辑器和解释器）。这个查看器将从图形库中构建，并提供当前通用无状态浏览器的功能，但也响应特定类型的数据和分子生物学特有的方法。在其他软件包（WPDB和PDBtool， http://www.cse.ogi.edu/DlSC/PDBTool/）中成功使用的显示对象之间的互操作性将提供适当级别的直观交互。提出的数据管理系统解决了当前一代支持分子生物学和许多其他学科的万维网服务器的局限性。值得注意的限制是：(i)保持服务器最新的困难；（二）信息内容广而不深；（iii）基于web的查询结果可视化工具受到交互的无状态特性和客户端和服务器之间计算资源不成比例的利用的限制和阻碍；（iv）可以扩展基于网络的蛋白质比较分析工具；(v)分子生物学家在建立和维护这类资源以供当地或全球使用方面几乎没有通用工具。

This project will develop a data management system to support a variety of data of importance to molecular biologists interested in groups of related proteins. The system will be distributed by the San Diego Supercomputer Center (SDSC) as part of an existing biological data resource supporting, among other things, data on the protein kinase family of enzymes (http://www.sdsc.edu/kinases) and temporal 3-dimensional structure data derived using X-ray crystallography. The system will permit queries integrating sequence homology, structure homology, function, and disease in a way not possible with the current generation of molecular biology resources. The overall goal is to provide to the community a non-proprietary system that is efficient, extensible and, for the molecular biologist, simple to use for loading their own data. These data could be subsets of data available from existing sources and/or their own private data. The system, will be coded in Java (or language of equivalent functionality), will run on a local computer or in a client-server environment using a local area network or the Internet. Specific deliverable are: (I) compact binary data storage, object oriented in-memory representation of macromolecular features, and query methodology suitable for analyzing comparative features found in proteins. This is an extension of technology already found in the software WPDB (http://www.sdsc.edu/CCMS/Packages/wpdb.html) and MOOSE (http://www.sdsc.edu/moose). (II) A client-server environment which is beyond the current stateless access provided by the World Wide Web. (III) Porting of existing methods written in C++ to Java and the creation of new methods providing an applet library for use in molecular biology. (IV) A low-level graphics library written in Java specifically for use in molecular biology. (V) A molecular biology viewer (i.e., a domain-specific browser, editor and interpreter). This viewer will be built from the graphics library and provide th e features of the current generalized stateless browsers, but also respond to specific types of data and methods peculiar to molecular biology. The interoperability between display objects, used successfully in other software packages (WPDB and PDBtool, http://www.cse.ogi.edu/DlSC/PDBTool/) will provide the appropriate level of intuitive interaction. The proposed data management system addresses limitations perceived in the current generation of World Wide Web-based servers supporting molecular biology and many other disciplines. Notable limitations are: (i) the difficulty of keeping servers current; (ii) the information content is broad but not deep; (iii) tools for visualizing results of Web-based query are limited and hampered by the stateless nature of the interaction and the disproportional utilization of computing resources between client and server; (iv) tools for the Web-based comparative analysis of proteins could be expanded; (v) there are few generic tools for the molecular biologist to use in building and maintaining this type of resource for either local or global use.