Abstract 5273: GenePattern Notebooks: an integrative analytical environment for cancer research
Authors: Reich Michael M. , Tabor Thorin , Liefeld John T. , Carr Peter , Hill Barbara , Nazaire Marc-Danie , Eby David , Thorvaldsdottir Helga , Tamayo Pablo , Mesirov Jill P. 
Published: July 2016

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” that included 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 (formerly IPython) Notebook system. GenePattern Notebook unites the phases of in silico research - experiment design, collaborative 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, or 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, serving as the complete, reproducible, in silico methods section for a publication. GenePattern Notebook also supports programmers and bioinformaticians, providing seamless interoperation between code blocks and GenePattern analyses within a notebook document. We are collaborating with cancer research laboratories to create GenePattern Notebook documents to serve as examples of integrative genomics research that can be enabled through this system. Potential notebook topics include characterization of intratumoral heterogeneity from single cell RNA-Seq data, effective clinical interpretation of comprehensive genomic profiling from whole exome sequencing of a patient's tumor and germ line samples, and identification of master regulators/transcription factors associated with the downstream transcriptional effects associated with the activation of an oncogene. We will make these and other notebooks available in an online GenePattern Notebooks repository, where other researchers may also contribute their notebooks.
Citation Format: Michael M. Reich, Thorin Tabor, John T. Liefeld, Peter Carr, Barbara Hill, Marc-Danie Nazaire, David Eby, Helga Thorvaldsdottir, Pablo Tamayo, Jill P. Mesirov. GenePattern Notebooks: an integrative analytical environment for cancer research. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5273.