XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services.
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services.
复制标题
DOI：
10.1186/1471-2105-10-279
复制
发表时间：
2009-09-04
影响因子：
3
通讯作者：
Wikberg JE
中科院分区：
文献类型：
--
作者：
Wagener J;Spjuth O;Willighagen EL;Wikberg JE
生命科学大量使用网络进行数据提供和分析。然而，越来越多的可用数据和分析工具的多样性要求机器可访问的接口，以便有效。基于HTTP的Web服务技术，如简单对象访问协议（SOAP）和表示状态传输（REST）服务，是当今生物信息学中最常用的技术。然而，这些方法有严重的缺点，包括缺乏可扩展性，以及服务无法发送状态通知。已经提出了几种互补的解决方案，但结果是质量不一的临时解决方案，可能难以使用。我们提出了一种新的方法，基于开放标准的可扩展消息传递和存在协议（XMPP），包括一个扩展（IO数据），包括发现，异步调用，并在服务中的数据类型的定义。XMPP云服务能够进行异步通信，这意味着客户端不必重复轮询状态，但是服务在完成时将结果发送回客户端。介绍了Bioclipse和Taverna的实现，以及生物和化学信息学中的各种XMPP云服务。XMPP及其扩展是一种强大的云服务协议，与传统的基于HTTP的Web服务相比，它具有以下几个优势：1）服务是可共享的，而不需要外部注册表，2）异步调用消除了对像轮询这样的ad-hoc解决方案的需要，以及3）在服务中定义的输入和输出类型允许在不需要外部语义描述的情况下即时生成客户端。与现有技术相比，XMPP具有许多优点，因此成为生物信息学中下一代在线服务的一个非常有趣的候选者。
Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use. We present a novel approach based on the open standard Extensible Messaging and Presence Protocol (XMPP), consisting of an extension (IO Data) to comprise discovery, asynchronous invocation, and definition of data types in the service. That XMPP cloud services are capable of asynchronous communication implies that clients do not have to poll repetitively for status, but the service sends the results back to the client upon completion. Implementations for Bioclipse and Taverna are presented, as are various XMPP cloud services in bio- and cheminformatics. XMPP with its extensions is a powerful protocol for cloud services that demonstrate several advantages over traditional HTTP-based Web services: 1) services are discoverable without the need of an external registry, 2) asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3) input and output types defined in the service allows for generation of clients on the fly without the need of an external semantics description. The many advantages over existing technologies make XMPP a highly interesting candidate for next generation online services in bioinformatics.
登录
查看更多内容
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
7
作者：
Hoon, S;Ratnapu, KK;Stupka, E
通讯作者：
Stupka, E
影响因子：
5.6
作者：
Dong, Xiao;Gilbert, Kevin E.;Wild, David J.
通讯作者：
Wild, David J.
HIV蛋白酶易感性的蛋白化学调查模型。
影响因子：
3
作者：
Lapins, Maris;Eklund, Martin;Spjuth, Ola;Prusis, Peteris;Wikberg, Jarl E. S.
通讯作者：
Wikberg, Jarl E. S.