The NEW Biology Workbench

描述(申请人提供)：生物医学研究已经变得越来越依赖软件和可视化工具来分析基因和蛋白质序列。提供适当的信息技术支持环境以分析序列和存储产生的数据是必不可少的，但对于以进行“湿实验室”调查为主要目标的研究人员来说，这往往是一个特别的挑战。目前，有28,000名研究人员和学生依赖生物工作台(workBench.sdsc.edu)来满足他们对序列分析软件、数据存储和数据检索的需求。生物学工作台为用户提供免费访问基于网络的环境，用户只需一个互联网浏览器就可以进行分析、访问数据库并存储他们的结果。用户可以使用80个序列分析功能和33个具有国际意义的远程数据库，并为其个人数据分配存储空间。生物学工作台的用户群现在已经超过了生物学工作台的原始体系结构所能支持的范围，并且其增长率保持不变。该提案概述了一种方法，以折射现有的生物学工作台，以创建一个更模块化、更稳定的平台，以满足分子生物学家对分析工具、数据库和存储其工作结果的区域的需求。在其重构的形式下，在这笔资金下创建的下一代生物学工作台将消除对用户数量的限制，创建一个易于扩展、可重复使用的结构，可以在其中安装社区代码。它将为用户提供访问所有当前可用的工作台工具和各种新的使能技术，包括可视化工具、Web服务、用户可配置的界面、对等数据共享功能和网格计算功能。该提案概述了创建和发展根据该提案创建的软件的明确方法，以确保其满足其用户群的需要。它还描述了将用户基础扩展到新社区的方法。

DESCRIPTION (provided by applicant): Biomedical research has become increasingly dependent upon software and visualization tools to analyze gene and protein sequences. Providing a proper information technology support environment to analyze sequences and store the data produced is essential, but often presents a particular challenge to researchers who have conducting "wet lab" investigations as their main goal. At present, 28,000 researchers and students depend on the Biology Workbench (workbench.sdsc.edu) to meet their needs for sequence analysis software, data storage, and data retrieval. The Biology Workbench provides users free access to web-based environment where users with only an internet browser can conduct analyses, access databases, and store their results. Users have access to 80 sequence analysis functions and 33 remote databases of international significance, and a storage allocation for their personal data. The user base of the Biology Workbench has now grown larger than the original architecture of the Biology Workbench can support, and its rate of growth remains constant. This proposal outlines a methodology to refractor the existing Biology Workbench to create a more modular, more stable platform to meet the needs of Molecular Biologists for analytical tools, databases, and an area to store the results of their work. In its refactored form, the Next Generation Biology Workbench created under this funding will remove the limitation on number of users, create an easily expansible, reusable structure into which community codes can be mounted. It will provide users access to all currently available Workbench tools, and a variety of new enabling technologies, including visualization tools, Web Services, a user configurable interface, peer-to-peer data sharing capabilities, and grid computing capabilities. The proposal outlines a well defined methodology for creating and evolving the software created under this proposal to ensure that it meets the needs of its user base. It also describes a methodology for expanding the user base into new communities.