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Cell Syst. 2017 Aug 23;5(2):149-151.e1. doi: 10.1016/j.cels.2017.07.003. Epub 2017 Aug 16.

The GenePattern Notebook Environment.

Author information

1
School of Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address: mmreich@cloud.ucsd.edu.
2
School of Medicine, University of California, San Diego, La Jolla, CA, USA.
3
The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
4
School of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
5
School of Medicine, University of California, San Diego, La Jolla, CA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

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.

KEYWORDS:

bioinformatics; integrative genomics; open science; reproducible research

PMID:
28822753
PMCID:
PMC5572818
DOI:
10.1016/j.cels.2017.07.003
[Indexed for MEDLINE]
Free PMC Article

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