基因表达谱分析工作簿环境。
The GenePattern Notebook Environment.
机构信息
School of Medicine, University of California, San Diego, La Jolla, CA, USA.
School of Medicine, University of California, San Diego, La Jolla, CA, USA.
出版信息
Cell Syst. 2017 Aug 23;5(2):149-151.e1. doi: 10.1016/j.cels.2017.07.003. Epub 2017 Aug 16.
Abstract
Interactive analysis notebook environments promise to streamline genomics research through interleaving text, multimedia, and executable code into unified, sharable, reproducible "research narratives." However, current notebook systems require programming knowledge, limiting their wider adoption by the research community. We have developed the GenePattern Notebook environment (http://www.genepattern-notebook.org), to our knowledge the first system to integrate the dynamic capabilities of notebook systems with an investigator-focused, easy-to-use interface that provides access to hundreds of genomic tools without the need to write code.
摘要
交互式分析笔记本环境通过将文本、多媒体和可执行代码交织到统一、可共享、可重复的“研究叙事”中，有望简化基因组学研究。然而，当前的笔记本系统需要编程知识，限制了研究界更广泛的采用。我们开发了 GenePattern Notebook 环境（http://www.genepattern-notebook.org），据我们所知，这是第一个将笔记本系统的动态功能与以调查员为中心、易于使用的界面集成的系统，该界面提供了对数百个基因组工具的访问，而无需编写代码。
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本文引用的文献
1
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Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2.
2
GenePattern 2.0.基因模式2.0
Nat Genet. 2006 May;38(5):500-1. doi: 10.1038/ng0506-500.
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