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

bioRxiv : the preprint server for biology
Authors
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.

Year of Publication
2023
Journal
bioRxiv : the preprint server for biology
Date Published
04/2023
DOI
10.1101/2023.04.04.535621
PubMed ID
37066251
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