The GenePattern Notebook Environment

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. [Display omitted] •We integrated the GenePattern genomics platform with the Jupyter Notebook environment•Notebooks interleave text, graphics, and analyses into complete “research narratives”•Users can embed genomic analyses into notebooks without the need to write code•GenePattern Notebook is freely available at http://www.genepattern-notebook.org Reich et al. have developed software that integrates the capabilities of electronic analysis notebooks and bioinformatics analysis portals. GenePattern Notebook uses the popular Jupyter Notebook platform that interleaves text, graphics, and code, and brings these tools for reproducible research, as well as access to hundreds of bioinformatics analyses, to non-programmers.