PT  - JOURNAL ARTICLE
AU  - Jiaming Hu
AU  - Ling-Hong Hung
AU  - Ka Yee Yeung
TI  - Embedding containerized workflows inside data science notebooks enhances reproducibility
AID  - 10.1101/309567
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 309567
4099  - http://biorxiv.org/content/early/2018/05/02/309567.short
4100  - http://biorxiv.org/content/early/2018/05/02/309567.full
AB  - Data science notebooks, such as Jupyter, combine text documentation with dynamically editable and executable code and have become popular for sharing computational methods. We present nbdocker, an extension that integrates Docker software containers into Jupyter notebooks. nbdocker transforms notebooks into autonomous, self-contained, executable and reproducible modules that can document and disseminate complicated data science workflows containing code written in different languages and executables requiring different software environments.