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A Visual Interface for on-the-fly Biological Database Integration and Workflow Design Using VizBuilder

机译：使用VizBuilder进行实时生物数据库集成和工作流程设计的可视界面

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Data integration plays a major role in modern Life Sciences research primarily because required resources are geographically distributed across continents and experts depend upon leveraging these digitally archived resources. The ever changing and exponentially growing digital archives pose a significant challenge for traditional data integration efforts and efficient development of data processing pipelines for scientific investigations. Thus a forceful argument can be made that in Life Sciences fast and ad hoc application design requiring data integration and workflow processing is urgently warranted. In this paper, we present a new visual application design toolkit, called VizBuilder, that can be used to design ad hoc applications at throw away costs by naive users in the Life Sciences to integrate remote databases and to design application pipelines. We leverage the recent development of BioFlow query language and LifeDB database management system that allows for such application design. We show that VizBuilder can be used as a front end query interface for LifeDB, with which robust and a wide range of applications can be developed at a very abstract and conceptual level without having to learn BioFlow. Users are able to express their application by drawing it using VizBuilder icons and connecting them in a meaningful way. Once completed, VizBuilder can compile and transform the visual application into an error-free BioFlow program to be executed in LifeDB. We present the functionality of VizBuilder using a real life application that our Life Sciences researchers have implemented and executed in LifeDB as part of their investigation.
机译：数据集成在现代生命科学研究中起着重要作用，主要是因为所需的资源在各大洲之间地理分布，并且专家依赖于利用这些数字存档的资源。不断变化和呈指数级增长的数字档案馆对传统的数据集成工作以及科学研究的数据处理管道的有效开发提出了重大挑战。因此，可以有力地论证，在生命科学中，迫切需要快速且临时的应用程序设计，要求进行数据集成和工作流处理。在本文中，我们提出了一个新的可视化应用程序设计工具包，称为VizBuilder，该工具包可用于生命科学领域的天真用户以抛弃成本设计临时应用程序，以集成远程数据库并设计应用程序管道。我们利用BioFlow查询语言和LifeDB数据库管理系统的最新开发来实现此类应用程序设计。我们展示了VizBuilder可以用作LifeDB的前端查询接口，通过该接口，可以在非常抽象和概念性的水平上开发强大而广泛的应用程序，而无需学习BioFlow。用户可以通过使用VizBuilder图标绘制应用程序并以有意义的方式连接它们来表达他们的应用程序。完成后，VizBuilder可以将可视应用程序编译并将其转换为要在LifeDB中执行的无错误的BioFlow程序。作为调查的一部分，我们使用生命科学的研究人员在LifeDB中实现并执行的现实生活应用程序来介绍VizBuilder的功能。

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