Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

Michael Reich; Thorin Tabor; John Liefeld; Jayadev Joshi; Forrest Kim; Helga Thorvaldsdottir; Daniel Blankenberg; Jill P Mesirov

doi:10.1101/2023.04.04.535621

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

bioRxiv [Preprint]. 2023 Apr 6:2023.04.04.535621. doi: 10.1101/2023.04.04.535621.

Authors

Michael Reich¹, Thorin Tabor¹, John Liefeld¹, Jayadev Joshi², Forrest Kim¹, Helga Thorvaldsdottir³, Daniel Blankenberg^{2

4}, Jill P Mesirov^{1

5}

Affiliations

¹ Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
² Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
³ The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
⁵ Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

Abstract

We present Genomics to Notebook (g2nb), an environment that combines the JupyterLab notebook system with widely-used bioinformatics platforms. Galaxy, GenePattern, and the JavaScript versions of IGV and Cytoscape are currently available within g2nb. The analyses and visualizations within those platforms are presented as cells in a notebook, making thousands of genomics methods available within the notebook metaphor and allowing notebooks to contain workflows utilizing multiple software packages on remote servers, all without the need for programming. The g2nb environment is, to our knowledge, the only notebook-based system that incorporates multiple bioinformatics analysis platforms into a notebook interface.

Publication types

Preprint

Abstract

Publication types

Grants and funding