Computational biomedicine: The role of workflow tools
Computational biomedicine: The role of workflow tools
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DOI：
10.1016/j.procs.2010.04.309
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发表时间：
2010-05
期刊：
影响因子：
--
通讯作者：
S. Zasada;P. Coveney
中科院分区：
文献类型：
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作者：
S. Zasada;P. Coveney
分布式和高性能计算越来越多地在医学研究中发挥作用，最终使用高性能和分布式计算的模拟可能用于支持常规临床决策。为了能够被生命科学家和医学家使用，并最终被临床医生使用，必须构建合适的工具来隐藏从数据采集到模拟再到分析的模拟链的大部分复杂性。许多这样的工具，自动化的模拟步骤的工作流程，近年来已被广泛开发。在本文中，我们分析了计算生物医学项目的需求，以揭示他们从工作流系统的关键，通用的要求。我们还将研究几个最流行的工作流系统，看看它们是否符合一般要求。最后，我们描述的工作流程和模拟环境，我们已经部署使用的虚拟生理人类倡议的研究人员，作为VPH工具包的一部分。
Distributed and high performance computing are increasingly finding a role in medical research and ultimately simulation using high performance and distributed computing is likely to be used to support routine clinical decision making. To be useable by life and medical scientists, and eventually by clinicians, suitable tools must be constructed which hide much of the complexity of the simulation chain, from data acquisition to simulation to analysis. Many such tools, which automate a workflow of simulation steps, have been extensively developed in recent years. In this paper we analyse the needs of computational biomedicine projects to uncover the key, generic requirements they have from a workflow system. We also look at several of the most popular workflow systems to see whether they meet the general requirements. We conclude by describing the workflow and simulation environment that we have deployed for use of Virtual Physiological Human Initiative researchers, as part of the VPH Toolkit.