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

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 platf...

Descripción completa

Detalles Bibliográficos
Autores principales: Reich, Michael, Tabor, Thorin, Liefeld, John, Joshi, Jayadev, Kim, Forrest, Thorvaldsdottir, Helga, Blankenberg, Daniel, Mesirov, Jill P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104038/
https://www.ncbi.nlm.nih.gov/pubmed/37066251
http://dx.doi.org/10.1101/2023.04.04.535621
_version_ 1785025958933168128
author Reich, Michael
Tabor, Thorin
Liefeld, John
Joshi, Jayadev
Kim, Forrest
Thorvaldsdottir, Helga
Blankenberg, Daniel
Mesirov, Jill P.
author_facet Reich, Michael
Tabor, Thorin
Liefeld, John
Joshi, Jayadev
Kim, Forrest
Thorvaldsdottir, Helga
Blankenberg, Daniel
Mesirov, Jill P.
author_sort Reich, Michael
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10104038
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Cold Spring Harbor Laboratory
record_format MEDLINE/PubMed
spelling pubmed-101040382023-04-15 Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis Reich, Michael Tabor, Thorin Liefeld, John Joshi, Jayadev Kim, Forrest Thorvaldsdottir, Helga Blankenberg, Daniel Mesirov, Jill P. bioRxiv Article 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. Cold Spring Harbor Laboratory 2023-04-06 /pmc/articles/PMC10104038/ /pubmed/37066251 http://dx.doi.org/10.1101/2023.04.04.535621 Text en https://creativecommons.org/licenses/by-nd/4.0/This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Reich, Michael
Tabor, Thorin
Liefeld, John
Joshi, Jayadev
Kim, Forrest
Thorvaldsdottir, Helga
Blankenberg, Daniel
Mesirov, Jill P.
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title_full Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title_fullStr Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title_full_unstemmed Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title_short Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
title_sort genomics to notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104038/
https://www.ncbi.nlm.nih.gov/pubmed/37066251
http://dx.doi.org/10.1101/2023.04.04.535621
work_keys_str_mv AT reichmichael genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT taborthorin genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT liefeldjohn genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT joshijayadev genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT kimforrest genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT thorvaldsdottirhelga genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT blankenbergdaniel genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis
AT mesirovjillp genomicstonotebookg2nbextendingtheelectronicnotebooktoaddressthechallengesofbioinformaticsanalysis

Ejemplares similares