Abstract 7426: The GenePattern ecosystem for cancer bioinformatics
Authors: Michael M. Reich, Thorin Tabor, John Liefeld, Edwin Huang, Forrest Kim, Jill P. Mesirov
Journal: Cancer Research (2024)

Abstract As the availability of genomic data and analysis tools from large-scale cancer initiatives continues to increase, with single-cell studies adding new dimensions to the potential scientific insights, the need has become more urgent for a software environment that supports the rapid pace of cancer data science. The GenePattern ecosystem, first introduced in 2004 and updated continually to support the changing needs of cancer genomics research, supports the analytical, computational, and reproducibility needs of the world-wide cancer analysis community.The GenePattern server, available at www.genepattern.org, provides hundreds of analysis methods for scientists at all levels of computational sophistication, with the only requirement for use being a web browser. The GenePattern server offers bulk and single-cell RNA-seq, copy number variation, flow cytometry, network analysis, general machine learning, gene set enrichment analysis, proteomics, and many other modalities. Analysis steps can be linked together into pipelines that can then be edited, shared, and made public. All parameters of an analysis, including the code version, are recorded so that an analytical result can be reproduced at any point in the future.The GenePattern Notebook system, notebook.genepattern.org, is an integration of the Jupyter Notebook environment with the GenePattern server. It combines the research narrative capabilities of Jupyter with the non-programming approach and breadth of analyses available in GenePattern. Scientists using GenePattern Notebook can create documents that include richly-formatted text and multimedia, executable code, and GenePattern analyses. A single GenePattern notebook can therefore comprise a sophisticated analytical workflow that runs on multiple remote servers.We have recently expanded GenePattern Notebook into a new notebook environment, Genomics to Notebook, g2nb.org, which adds the ability to include analyses on any public Galaxy server as well as using the Integrative Genomics Viewer (IGV) and Cytoscape within notebooks. Each analysis or visualization appears a cell within a notebook, preserving the accessibility and ease of use of the notebook metaphor while retaining the essential aspects of each tool’s user interface. When run, the entire analysis appears to execute seamlessly within the notebook. The online workspace also includes a library of featured genomic analysis notebooks, including templates for common analysis tasks as well as cancer-specific research scenarios and compute-intensive methods. Scientists can easily copy these notebooks, use them as is, or adapt them for their research purposes. Citation Format: Michael M. Reich, Thorin Tabor, John Liefeld, Edwin Huang, Forrest Kim, Jill P. Mesirov. The GenePattern ecosystem for cancer bioinformatics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7426.