Scientific workflow systems: Pipeline Pilot and KNIME.
Scientific workflow systems: Pipeline Pilot and KNIME.
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DOI：
10.1007/s10822-012-9577-7
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发表时间：
2012-07
影响因子：
3.5
通讯作者：
Warr, Wendy A.
中科院分区：
文献类型：
--
作者：
Warr, Wendy A.
有许多科学工作流系统的例子[1，2]；在这篇简短的文章中，我将只集中在化学信息学应用程序和化学信息学中最常用的工作流工具，即管道试点[3]和Knime[4]。多年来，工作流解决方案已经在生物信息学和其他科学中使用，一些解决方案还应用于所谓的“商业智能”和“预测分析”。读者可以在网上找到Discovery Net、Galaxy、Kepler、Triana、SOMA、SMILA、VisTrails和其他网站的详细信息。Kappler比较了竞争工作流、Taverna和管道试点[5]。Taverna已被广泛用于生物信息学，但也与化学开发工具包(CDK)一起使用[6，7]。CDK-Taverna工作流可在MyExament上免费使用。Org[8]。(我的实验。发现网是最早的科学工作流系统之一；它的概念后来在InforSense知识发现环境(KDE)中商业化。我2007年的评论[1]集中在管道试点和InforSense KDE上；Knime当时还是一个相对较新的参与者。2009年，亏损的InforSense组织被IDBS收购，KDE在转化医学方面取得了进展[9]。InforSense的ChemSense[10]使用了ChemAxon的JChem Cartridge，以及ChemAxon的化学结构、属性预测和枚举工具。ChemSense的三个主要制药客户已经转向其他解决方案。InforSense Suite仍然存在，但它并不被视为“个人生产力工具”；相反，它被集成到IDBS ELN平台中。Knime和
There are many examples of scientific workflow systems [1, 2]; in this short article I will concentrate only on cheminformatics applications and the workflow tools most commonly used in cheminformatics, namely Pipeline Pilot [3] and KNIME [4]. Workflow solutions have been used for years in bioinformatics and other sciences, and some also have applications in so-called ‘‘business intelligence’’and ‘‘predictive analytics’’. Readers can find details of Discovery Net, Galaxy, Kepler, Triana, SOMA, SMILA, VisTrails, and others on the Web. Kappler has compared Competitive Workflow, Taverna and Pipeline Pilot [5]. Taverna has been widely used in bioinformatics but is also used with the Chemistry Development Kit (CDK)[6, 7]. CDK-Taverna workflows are made freely available at myExperiment. org [8].(myExperiment. org also includes KNIME workflows.)DiscoveryNet was one of the earliest examples of a scientific workflow system; its concepts were later commercialized in InforSense Knowledge Discovery Environment (KDE). My 2007 review [1] centered on Pipeline Pilot and InforSense KDE; KNIME was then a relative newcomer. In 2009 the loss-making InforSense organization was acquired by IDBS and KDE has made progress in translational medicine [9]. InforSense’s ChemSense [10] used ChemAxon’s JChem Cartridge, and ChemAxon chemical structure, property prediction, and enumeration tools. ChemSense’s three major pharmaceutical customers have turned to other solutions. The InforSense Suite lives on but it not seen as a ‘‘personal productivity tool’’; rather it is integrated into the IDBS ELN platform. KNIME and
影响因子：
5.6
作者：
Patel, Hina;Bodkin, Michael J.;Gillet, Valerie J.
通讯作者：
Gillet, Valerie J.
影响因子：
8.6
作者：
Truszkowski, Andreas;Jayaseelan, Kalai Vanii;Steinbeck, Christoph
通讯作者：
Steinbeck, Christoph
影响因子：
3
作者：
Kuhn T;Willighagen EL;Zielesny A;Steinbeck C
通讯作者：
Steinbeck C