Li Peter, Oinn Tom, Soiland Stian, Kell Douglas B
School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, UK.
Bioinformatics. 2008 Jan 15;24(2):287-9. doi: 10.1093/bioinformatics/btm578. Epub 2007 Dec 1.
Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model.
Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net
许多数据处理过程都涉及使用编程库。由于这些过程会被重复使用，因此对其进行自动化处理可能会带来益处。一种便捷的自动化形式是工作流，它还允许此类过程在社区中共享。Taverna工作流系统已得到扩展，使其能够在Taverna工作流中使用和调用Java类及方法作为任务。这些类和方法是在工作流构建期间由一个名为API消费者的Java Doclet应用程序选择使用的。此选择存储为一个XML文件，该文件使Taverna能够呈现API的子集以供在工作流组合中使用。我们通过一个工作流展示了Taverna调用Java类和方法的能力，在该工作流中我们使用libSBML将基因表达数据映射到一个表示为SBML模型的代谢途径上。
Taverna和API消费者应用程序可从http://taverna.sourceforge.net免费下载
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