Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
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DOI：
10.1186/1471-2105-6-87
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发表时间：
2005-04-07
影响因子：
3
通讯作者：
Ragan MA
中科院分区：
文献类型：
--
作者：
Garcia Castro A;Thoraval S;Garcia LJ;Ragan MA
解决问题的计算方法需要在特定问题的工作流程中交织信息访问和算法执行。这些工作流程的结构是由能够表示它们的句法、语义和代数对象的支架定义的。尽管生物信息学中 GUI（图形用户界面）不断涌现，但只有其中一些提供工作流程功能；令人惊讶的是，尚未报道生物信息学中工作流程操作符和组件的荟萃分析。我们提出了一组能够表示生物信息学中的分析工作流程的句法组件和代数运算符。迭代、递归、条件语句的使用以及挂起/恢复任务的管理传统上都是临时实现的并且是硬编码的；通过正确定义这些运算符，可以将它们作为通用可重用组件来使用和参数化。为了说明如何编排这些操作，我们提出了 GPIPE，它是 PISE 的原型图形管道生成器，它允许定义管道、对其组件方法进行参数化以及以 XML 格式存储元数据。此实施超出了 PISE 当前的宏功能。由于整个分析协议都是用 XML 定义的，因此可以在用户之间复制或共享完整的生物信息学实验（方法、参数和结果的链接集）。可用性：（交互式），（下载）。从我们的荟萃分析中，我们确定了生物信息学中许多工作流程常见的句法结构和代数运算符。工作流组件和代数运算符可以被同化为可重用的软件组件。 GPIPE 是该框架的原型实现，提供了一个 GUI 构建器来促进工作流程的生成和异构分析工具的集成。
Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools.
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影响因子：
5.8
作者：
Letondal, C
通讯作者：
Letondal, C
影响因子：
3
作者：
Shah SP;He DY;Sawkins JN;Druce JC;Quon G;Lett D;Zheng GX;Xu T;Ouellette BF
通讯作者：
Ouellette BF
影响因子：
5.8
作者：
Ernst, P;Glatting, KH;Suhai, S
通讯作者：
Suhai, S
影响因子：
5.8
作者：
Stevens, Robert D.;Robinson, Alan J.;Goble, Carole A.
通讯作者：
Goble, Carole A.
影响因子：
5.4
作者：
Sowa, JF
通讯作者：
Sowa, JF