Abstract 5106: The GenePattern Notebook environment for reproducible cancer research
Authors: Reich Michael M. , Tabor Thorin T. , Liefeld Ted , Hill Barbara , Thorvaldsdottir Helga , Mesirov Jill P. 
Published: August 2019

Abstract
As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more urgent for a software environment that supports the entire “idea to dissemination” cycle of an integrative cancer genomics analysis. Such a system would need to provide access to a large number of analysis tools without the need for programming, be sufficiently flexible to accommodate the practices of non-programming biologists as well as experienced bioinformaticians, and would provide a way for researchers to encapsulate their work into a single executable document including not only the analytical workflow but also the associated descriptive text, graphics, and supporting research. To address these needs, we have developed GenePattern Notebook, based on the GenePattern environment for integrative genomics and the Jupyter Notebook system. GenePattern Notebook unites the phases of in silico research - experiment design, analysis, and publication - into a single interface.
GenePattern Notebook presents a familiar lab notebook format that allows researchers to build a record of their work by creating cells containing text, graphics, and executable analyses. Researchers add, delete, and modify cells as the research evolves, supporting the initial research phases of prototyping and collaborative analysis. When an analysis is ready for publication, the same document that was used in the design and analysis phases becomes a research narrative that interleaves text, graphics, data, and executable analyses. The online notebook format allows researchers to explain the analytical and scientific considerations of each step in any level of detail, promoting reproducibility and adoption.
GenePattern Notebook features are designed to help nonprogramming users. We have developed additional cell types allowing users to select analyses, specify inputs, navigate results, send result files to new analyses, and create richly formatted text, all without the need for programming.
The GenePattern Notebook Environment is also a platform for open science and reproducible research. Authors can elect to publish a notebook, making it visible to all users, who can then create a copy and use it to reproduce the author’s results or adapt it to their own work. The repository provides links to public notebooks that can be used in a publication as permalinks. Researchers can invite collaborators to work together on a notebook prior to publication.
A free, cloud-based GenePattern Notebook workspace is available at http://www.genepattern-notebook.org, where researchers can develop, share, and publish notebook documents. We have provided a collection of template notebooks that walk users through various genomic and machine learning analyses, and are collaborating with research laboratories to create integrative cancer genomics notebooks.
Note: This abstract was not presented at the meeting.
Citation Format: Michael M. Reich, Thorin T. Tabor, Ted Liefeld, Barbara Hill, Helga Thorvaldsdottir, Jill P. Mesirov. The GenePattern Notebook environment for reproducible cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5106.