Automated manipulation of systems biology models using libSBML within Taverna workflows
Automated manipulation of systems biology models using libSBML within Taverna workflows
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DOI：
10.1093/bioinformatics/btm578
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发表时间：
2008-01-15
期刊：
影响因子：
5.8
通讯作者：
Kell, Douglas B.
中科院分区：
文献类型：
--
作者：
Li, Peter;Oinn, Tom;Kell, Douglas B.
许多数据操作过程都涉及到编程库的使用。这些过程由于其重复使用而可以有利地自动化。一种方便的自动化类型是工作流的形式，它也允许这些过程在社区中共享。Taverna工作流系统已经扩展，使其能够使用和调用Java类和方法作为Taverna工作流中的任务。这些类和方法是由称为API Consumer的Java Doclet应用程序在工作流构造期间选择使用的。此选择存储为XML文件，使Taverna能够呈现API的子集，以用于工作流的组合。Taverna调用Java类和方法的能力证明了一个工作流程，在该工作流程中，我们使用libSBML映射基因表达数据到代谢途径表示为SBML模型。
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.