An Online Provenance Service for Distributed Metabolic Flux Analysis Workflows

T. Dalman, M. Weitzel, W. Wiechert, Bernd Freisleben, K. Nöh
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引用次数: 4

Abstract

Scientific applications in the area of Systems Biology become more and more demanding in terms of workflow organization and required computational resources. Metabolic flux analysis with carbon tracer experiments (13C-MFA) is a particularly challenging technology consisting of several tightly interwoven building blocks, some of which are quite compute-intensive while others may require human expert interaction. Within these buildings blocks and at their interfaces, large amounts of provenance data (i.e., process messages, logs and metadata) are created. An online provenance approach for a scientific workflow framework is presented to efficiently monitor and analyze long running parallel 13C-MFA applications. The design of our approach consists of a cross-language programming interface for generating messages, a provenance store for collecting log messages from distinct workflows, and a versatile user client for querying and filtering data of interest. Seamless integration into the BPEL-based scientific workflow framework is enabled by web service interfaces. Salient features of our provenance solution are interactivity and scalability, as demonstrated by two examples. The framework provides the capability to capture, filter, query, and trace provenance data on demand. Our solution leverages scientific analysis of complex 13C-MFA workflows.
分布式代谢通量分析工作流的在线溯源服务
系统生物学领域的科学应用对工作流组织和所需的计算资源的要求越来越高。碳示踪实验代谢通量分析(13C-MFA)是一项特别具有挑战性的技术,由几个紧密交织的构建块组成,其中一些是相当密集的计算,而另一些可能需要人类专家的交互。在这些构建块及其接口中,创建了大量的来源数据(即,流程消息、日志和元数据)。提出了一种科学工作流框架的在线溯源方法,以有效地监控和分析长时间运行的并行13C-MFA应用程序。我们的方法的设计包括一个用于生成消息的跨语言编程接口,一个用于从不同工作流收集日志消息的来源存储,以及一个用于查询和过滤感兴趣数据的通用用户客户端。web服务接口支持与基于bpel的科学工作流框架的无缝集成。我们的溯源解决方案的显著特性是交互性和可伸缩性,正如两个示例所演示的那样。该框架提供了按需捕获、过滤、查询和跟踪来源数据的功能。我们的解决方案利用了对复杂的13C-MFA工作流程的科学分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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