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

机译:用于现场生物数据库集成和使用VizBuilder的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,主要研究,因为所需的资源在大陆地理分布和专家取决于利用这些数字归档资源的重大作用。在不断变化的,成倍增长的数字档案构成了传统的数据集成工作和数据处理管道用于科学研究高效发展的一个显著的挑战。因此,一个有说服力的论点,可以提出,在生命科学快速和即席应用程序设计需要数据集成和工作流处理迫切必要。在本文中,我们提出了一种全新的视觉应用设计工具包,叫做VizBuilder,可以使用通过在生命科学天真的用户设计的扔掉成本特设应用集成远程数据库,并设计应用管道。我们利用最近的BIOFLOW查询语言和LifeDB数据库管理系统,允许这样的应用的设计开发。我们表明,VizBuilder可以作为一个前端查询界面LifeDB,与强大的和广泛的应用可以在一个非常抽象和概念层面上开发,而无需学习BIOFLOW。用户可以通过绘制它使用VizBuilder图标并将其以有意义的方式连接到表达自己的应用程序。一旦完成,VizBuilder可以编译和改造视觉应用到LifeDB要执行的无差错BIOFLOW程序。我们提出VizBuilder的使用实际生活中的应用,我们的生命科学的研究人员已经实现并作为调查的一部分在LifeDB执行的功能。

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