BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

Denis Torre; Alexander Lachmann; Avi Ma'ayan

doi:10.1016/j.cels.2018.10.007

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

Cell Syst. 2018 Nov 28;7(5):556-561.e3. doi: 10.1016/j.cels.2018.10.007. Epub 2018 Nov 14.

Authors

Denis Torre¹, Alexander Lachmann¹, Avi Ma'ayan²

Affiliations

¹ Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai Center for Bioinformatics, Knowledge Management Center (KMC) for Illuminating the Druggable Genome (IDG), Team Nitrogen of the NIH Data Commons Pilot Project Consortium (DCPPC), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
² Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai Center for Bioinformatics, Knowledge Management Center (KMC) for Illuminating the Druggable Genome (IDG), Team Nitrogen of the NIH Data Commons Pilot Project Consortium (DCPPC), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA. Electronic address: avi.maayan@mssm.edu.

Abstract

BioJupies is a web application that enables the automated creation, storage, and deployment of Jupyter Notebooks containing RNA-seq data analyses. Through an intuitive interface, novice users can rapidly generate tailored reports to analyze and visualize their own raw sequencing files, gene expression tables, or fetch data from >9,000 published studies containing >300,000 preprocessed RNA-seq samples. Generated notebooks have the executable code of the entire pipeline, rich narrative text, interactive data visualizations, differential expression, and enrichment analyses. The notebooks are permanently stored in the cloud and made available online through a persistent URL. The notebooks are downloadable, customizable, and can run within a Docker container. By providing an intuitive user interface for notebook generation for RNA-seq data analysis, starting from the raw reads all the way to a complete interactive and reproducible report, BioJupies is a useful resource for experimental and computational biologists. BioJupies is freely available as a web-based application from http://biojupies.cloud.

Keywords: Data Commons; Jupyter Notebook; RNA-seq; bioinformatics; data visualization; enrichment analysis; pipeline; systems biology.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Computational Biology / methods*
High-Throughput Nucleotide Sequencing / methods
Humans
Mice
Sequence Analysis, RNA / methods*
Software*

Abstract

Publication types

MeSH terms

Grants and funding