GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.
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DOI：
10.1186/1471-2105-9-s4-s13
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发表时间：
2008-04-25
影响因子：
3
通讯作者：
Giegerich R
中科院分区：
文献类型：
--
作者：
Lamprecht AL;Margaria T;Steffen B;Sczyrba A;Hartmeier S;Giegerich R
PCR引物的设计是一个日常的，但不是琐碎的任务，需要最先进的软件。我们描述了流行的工具GeneFisher，并解释了它最近使用工作流技术进行的重组。我们采用面向服务的方法来建模和实现GeneFisher- p，这是GeneFisher web应用程序的一个基于流程的版本，作为Bio-jETI平台的一部分，用于服务建模和执行。我们将展示如何引入灵活的流程层，以满足对改进的用户友好性和灵活性日益增长的需求。在Bio-jETI中，我们使用jABC框架（一个成熟的模型驱动的、面向服务的流程定义平台）对流程进行建模。我们使用jETI封装远程遗留工具并集成web服务，jETI是jABC的扩展，用于将远程资源无缝集成为基本服务，准备在流程中使用。GeneFisher使用的一些基本服务实际上已经作为BiBiServ的个人web服务提供，并且可以直接访问。其他是遗留程序，并通过jETI技术提供给Bio-jETI。当更多的生物信息学工具（可作为web服务或通过jETI获得）导致基本过程的简单扩展或变化时，就需要基于服务的面向过程的全部功能。这涉及到由欧洲生物信息学研究所（EBI）提供的数据检索或校准工具的变化。由此产生的面向服务和流程的GeneFisher-P演示了如何在Bio-jETI平台中轻松地编排来自异构源的基本服务，并导致针对特定任务定制的灵活的专门流程系列。
PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). The resulting service- and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.